What I did to apparently solve the problem.
In snowboard I unselected the hide icon option since I had turned it on.
This makes it so that it doesn't hide the icon, which probably taps into the libhide settings in order for it to work.
Note: I had gotten rid of springboard while trying to solve the problem. I had to reinstall it just to find out that that particular hide setting was automatically on. So the settings were still saved somewhere even though I had uninstalled it.
With that in mind I proceeded to uninstall winterboard again.
Then went back to cydia and uninstalled, from the package section under manage, the preferenceloader by bigboss. I figured it was this what allowed it to remember the setting I mentioned before.
Doing this will not let you play with around with themes and stuff like that, but it's a way to really get rid of the icons for sure. At least that's what I think for now.
I never actually tried to simply turn off 'hide winterboard icon' and then go from there, I really just wanted to get rid of them, maybe I'll try later.
Last: you can just forget about them build a folder just for them and put it somewhere it won't bother you, I'm running iOS 4.0.