Whether it matters depends a lot on how competitive the market is. If your app is head and shoulders above the competition in functionality, users will put up with a little UI ugliness. If most of the apps in your market basically do everything the user wants, they're going to decide based on what is prettiest/most responsive, which is usually the native app.

I still remember discovering uTorrent. I'd tried about 4-5 Bittorrent apps before then, including 3 wxPython-based ones and Azureus. They also basically did what I needed - they let me download, they let me keep track of existing transfers, and they let me throttle bandwidth. The difference was that uTorrent didn't take up a few hundred megs of RAM and didn't peg my CPU. The developer accomplished this by doing an end-run around all the layers of abstraction and keeping an eye on performance; it's much harder to do this with a cross-platform library in the way.