Yes, but USB tuner usually has less sensitivity than PCI version and might not be strong enough to pick up some of the weaker stations, whereas a PCI(e) card might.
The tuner sensitivity should be your primary focus, however. Not whether it's USB or PCI. Some higher-end USB tuners are better than junk PCI tuners, but overall PCI tuner will perform better.
Back to the case though, as long as the case doesn't mention "low-profile PCI" anywhere you should be fine. Look for pictures of the rear of the case online and you will be able to tell the difference.
The picture below is of the Silverstone LC15. It's a horrible case, but it shows both "low profile" options: horizontal "Full Height PCI" (via riser card that is not shown) in the middle left and vertical "low-profile PCI" slots on the far left. Most cases will have one or the other, not both.
Just make sure if you have full height cards, your case has full-height slots or if you get a case that only has low-profile slots, your cards have low-profile brackets.