If you've already updated to iTunes 11.0.4 and it's still not working, uninstall and reinstall iTunes and it's components. http://support.apple.com/kb/ht1923
If that still doesn't work, it's possible your antivirus/security software is blocking it. Temporarily disable it to see if it's appearing.
If it's still not appearing, temporarily disable everything in your computer but iTunes and essential windows components and slowly start adding things till you find the exact process blocking your iPhone. http://support.apple.com/kb/HT2292
Short answer: Nope
Long answer: Nope, nada, not at all, zippo
Longer answer: Uninstalling iTunes removes the system components for iTunes, however it doesn't remove the iTunes media folder located in your user library. When you install iTunes, the first thing it does is look for an iTunes media folder. If it finds one, it'll allow you to import your music/apps/etc. If it doesn't find one, it creates a new one