No, don't be ridiculous! Attempting to 'explain' "p's and q's" by reference to an imagined possessive is really reaching! (Anyway, the "pints and quarts" 'explanation' is not the only possibility - another is that it refers to typesetters' letters, where you have to be careful to pick the correct one, since of course they appear in reverse, and in a serif font can look very similar.) But "p's and q's" was merely a common example: the OED agrees that if I need to refer to multiple f's or g's (or 5's) I can use an apostrophe to do so.

I don't think anything of "C.D.s". CD is the generally accepted spelling, and I think C.D. thus looks unusual if not unnatural. As I keep saying, CDs is a perfectly good plural (as long as one has access to both upper and lower case letters) and I see no need to try to coin a new one; merely, I accept CD's as a valid alternative, even though I personally don't favour it. If writing in all-caps, C.D.S suffers the exact same problem as CDS, or perhaps even more so.