APL (Dyalog), 60 59 bytes

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charge magnitudes as right argument.

{∊(⍺{⍵∧1<≢⍺∩⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵} 

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{…} anonymous lambda where ⍺ and ⍵ represent the left and right arguments:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍺∩ intersection of ion and that

≢ tally the number of characters in that

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍵∧ and do we need multiple of that ion?

: if so, then:

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)

APL (Dyalog), 60 59 61 bytes

+2 since charges must be given signed.

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charges as right argument.

{∊(⍺{⍵∧1<≢⍺∩⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵}∘| 

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{…}∘| function where ⍺ is left argument and ⍵ is right argument's magnitude:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍺∩ intersection of ion and that

≢ tally the number of characters in that

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍵∧ and do we need multiple of that ion?

: if so, then:

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)

APL (Dyalog), 60 59 bytes

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charge magnitudes as right argument.

{∊(⍺{⍵∧1<≢⍺∩⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵} 

Try it online!

{…} anonymous lambda where ⍺ and ⍵ represent the left and right arguments:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍵∩ intersection of ion and that

≢ tally the number of characters in that

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍺∧ and do we need multiple of that ion?

: if so, then:

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)

APL (Dyalog), 60 59 bytes

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charge magnitudes as right argument.

{∊(⍺{⍵∧1<≢⍺∩⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵} 

Try it online!

{…} anonymous lambda where ⍺ and ⍵ represent the left and right arguments:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍺∩ intersection of ion and that

≢ tally the number of characters in that

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍵∧ and do we need multiple of that ion?

: if so, then:

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)

APL (Dyalog), 60 bytes

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charge magnitudes as right argument.

{∊(⍺{⍵∧1<+/⍺∊⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵} 

Try it online!

{…} anonymous lambda where ⍺ and ⍵ represent the left and right arguments:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍵∊ for each character of the ion, check whether a member of that

+/ sum

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍺∧ and we need multiple of that ion

: then

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)

APL (Dyalog), 60 59 bytes

Anonymous infix function. Takes list of ions (anion, cation) as left argument and list of corresponding charge magnitudes as right argument.

{∊(⍺{⍵∧1<≢⍺∩⎕D,⎕A:1⌽')(',⍺⋄⍺}¨m),¨(m←s≠1)/¨'_',∘⍕¨s←⍵÷⍨∧/⍵} 

Try it online!

{…} anonymous lambda where ⍺ and ⍵ represent the left and right arguments:

∧/⍵ LCM of the charges

⍵÷⍨ divide the charges by that

s← store in s (for subscripts)

'_',∘⍕¨ format (stringify) and prepend underbar to each

(…)/ replicate each letter of each with the corresponding value from:

s≠1 Is s different from 1? (gives 1 or 0)

m← store in m (for multiple)

(…),¨ prepend the following respectively to those:

⍺{…}¨m for each, call this function with ions and m as arguments:

⎕D,⎕A Digits followed by uppercase Alphabet

⍵∩ intersection of ion and that

≢ tally the number of characters in that

1< Is one less than that? (i.e. do we have a multi-element ion?)

⍺∧ and do we need multiple of that ion?

: if so, then:

')(',⍺ prepend the string to the ion

1⌽ cyclically rotate one step to the left (puts ) on the right)

⋄ else

⍺ return the ion unmodified

∊ ϵnlist (flatten)