Comment 10 for bug 208079

It seems that part of this problem has been aknowledged by inkscape developers and that a fix is on the way:

http://codewideopen.blogspot.com/2008/04/freedom-from-size-tyrany.html

According to the above page, many of the issues with size are due to the use of custom toolbars from before GTK+ had stock ones and the fact that preferences to make toolbar smaller have no effect on Ubuntu.

A specific bug report was opened https://bugs.launchpad.net/inkscape/+bug/221676 and now has in progress status.

Let us hope that this at least mitigates the size issues in inkscape.