You certainly can. You can make a character style for the subscripts. I suggest, of there isn’t already a subscript available in the font you bump the weight up a bit. I also suggest using horizontal and vertical sclaing rather than changing the point size. You get finer control and the scaling will scale with the point size.
In the bleow image I have three columns. On the left is your supplied text with no formatting applied. In the middle I have changed all the numbers to use the Subscript/Inferior form included in the font Minion Pro I applied this style using GREP Styles. On the right I created a character style for the subscript by adjusting the baseline, horizontal and vertical scale, and weight. I applied the subscript using GREP.
You can view the GREP expression below. I just used the wildcard for any digit.
I have a document which has nos. init but they are not a part of chemical formulas. Example: we have category nos (A297C12, N3034F1) which I don't need any subscript and we have the chemical formulas all over the document, and it's around a 100-page brochure.