I find reduced size windows to work fine on 1280x800, i have to move the window up a tiny bit to reach the top buttons, or move the taskbar to the left, however expect it would still be a problem on 1024x768.
There is another method i found worked well if all else fails, just go to desktop properties, settings, advanced, monitor, and untick the box that says [hide modes this monitor can not display], click apply then go back to the settings tab and you should be able to set your desktop resolution higher than your monitor can display as long as your video card can still create that resolution.
In effect you get a scrolling desktop which will easily allow you to reach the buttons at the bottom, no problem. I only used it on 1280x800 and only needed to reach the bottom, i expect on 1024 wide you might be a little annoyed going left or right on most windows to reach certain buttons, but it should still be playable.
Note this display hack only seems to work on XP, i couldn't get vista to let me uncheck that box, it's possible but i couldn't wrap my head around the workaround.
Also that ninja ship idea sounds good I'm still on my first game and have finished using spacemaster to mess around with these proxima centauri aliens, i discovered they are precursors and therefore only have a handful of ships which i can deal with after a few more tech levels, i popped a 1k ton probe over the jump point just in case and am researching FACs, microwaves new engines and more powerful warheads, you see where this is going?
get close, disable drive, then fire some long range size 100 warheads at em, heh
(in SM mode i sugessfully used size 100 warheads against his mere 7500 ton ships, results were impressive when they hit( crew training and drive speed made the biggest difference in accuracy) having finished learning combat and their capabilities i save scummed and went back to Turtling and learning the interface