It's been way too long since I used InDesign CS4, but I don't remember that being a problem back then.
In more recent versions of InDesign I have installed (CS5.5 and CS6), there seems to be no problem.
Here are two versions of Optima (T1 and TT):
Here are three versions of Zapf Dingbats (OT, TT and T1):
If there were a problem in CS4, your best bet is to do a workaround as you have done. There won't be a bug fix for it.
A lot depends on the internal file naming in the fonts. If they have the same name that ID is reading, then there is a problem. Most OT fonts with Postscript outlines are named as Std or Pro at the end, and ID has no problem distinguishing them, but many based on TT outlines, especially from Microsoft show the old TT names and caue problems when they are installed next to another font with the same name.