There are some things that apple does right. There also many things apple does WRONG.
A few things with what your experiencing:
1) It has absolutely nothing to do with a 500gb hard drive. I have a library of over 10,000 mp3s loaded in iTunes and it runs fine off of a secondary (internal) hard drive. Either that or your hard drive has a serious problem (being really slow), which I really doubt is even possible, as I've never heard of such a thing. Or, it could be that you're running on USB 1.0, which, even then is impossible because the XML library file is loaded from your internal hard drive, and simply accessing a small 3-5mb mp3 file does not lag, even on USB 1.0.
2) When you load any track into iTunes, it automatically gets checked for album art and gapless playback/being part of a compilation. There is no way to turn off this feature. While this happens, it slows down every process in iTunes significantly. Now, since you loaded 3,500 mp3s, these could still be getting the album art/gapless check running in the background AFTER theyve been added to the library. This takes significantly longer than just having the tracks get added to the library. Some people dont care about album art or gapless, therefor apple needs to implement a feature to turn this OFF.
3) You may have noticed that with each new version of iTunes, its become more and more bloated with crap most of us don't use (iTunes Music Store, Apps store, TV shows, podcasts, genius, ipod/iphone support, etc). iTunes is not exactly a processor/memory friendly application, so don't be too bummed if it runs slow, its a poor application nowadays, which should be renamed to iMedia for having all the excess crap thrown onto it.
As always, I'd suggest using an alternative application. For now, there really isnt anything (sad, because the mac is so highly regarded as a media computer) however, the next release of 'Vox' will have a fully working library for adding mp3s. When this is released, I am never returning to iTunes. Check it out:
www.voxapp.net