We had to replace a number of saloon windows due to cracking and the resultant leaks. The acrylic windows weren''t in a frame, just stuck with silicone on fiberglass and w/some thru-bolts. At least the OEM made those OEM hole locations solid fiberglass (unlike all the other hole locations on deck).
We went for a Lexan replacement, even though we weren''t able to find Lexan as deeply tinted as the OEM acrylic. Lexan is tough stuff! Our windows cost about USD 300 and should last much longer to boot. (Well, now that the boat doesn''t flex in three directions anymore... but the structural issues are another story)
Anyway, I am a true believer of Lexan. If your surfaces don''t curve excessively, I''d replace everything w/Lexan. You''ll sleep better in a bad storm.
Besides, if your topsides are cored, then thru-bolting exterior Lexan windows properly is a real PIA - that is unless you don''t mind rotting the core through hundreds of little bolt holes. Every hole will have to be overdrilled, epoxied, redrilled, and the end result is unlikely to look good unless you repaint the topsides.