This is normal, I'm pretty sure. This is how the N900 works - it has three partitions (four if you count swap); a rootfs partition, the /home (the whole optification thing, with the /opt directory, is part of this), which is the one you're referring to, and by default it's only 2GB, and the MyDocs partition, which is the remaining almost-30GB of space. Applications don't count this as part of "space to install apps", but most apps also put as much as they can out of rootfs into /opt, and as much as they can from /opt into the MyDocs part, to conserve room.

Assuming you knew all this, what's the problem? The N900, if I recall correctly, has about this much space taken up by default by all the stuff preinstalled on it. That said, most of this isn't exactly bad, because a lot of the preinstalled stuff is libraries that other apps use.

Also, if you stay within the apps in Extras, and don't go into Testing or Devel, you shouldn't have too many problems with apps filling up that 2GB too quickly.

I might be wrong about the above of course, but I think that's all there is to it.