I’m not sure I noticed much when I bought mine – road and mtb.
I got a lovely set of DT EX471 wheels built up for my Trigger Carbon last year. PT Cycles did a terrific job. I’m n to convinced I could tell the difference between those and my so called flexy stock wheels. Maybe I’m not aggressive or heavy enough. The ARC27 on my current bike gets middling reviews but I’m perfectly happy with them.
I also bought a pair of Fulcrum Carbon Disc wheels for my road bike – cheap for brand name carbon, but still very expensive in comparison to a good pair of alloy MTB wheels (I never thought I’d spend so much). Not convinced I can tell difference there either. Maybe slightly more responsive and maybe a little less vibration – not sure. I got them last year just before a serious amount of work travel kicked in and I didn’t really get to spend much time on the bike – so hard to remember what it was like on the old wheels. They look fantastic though. :)
I guess my answer is maybe. Especially if you have really really heavy wheels stock or you just broken a wheel, then I’d be more inclined to buy a nice upgrade than a cheap replacement.