This may sound amateurish, as odf tweaking seems to be a thing of the past with portings from BC to Legacy. Nevertheless, I've noticed that tinkering with the hull and shield levels of the individual ship's odf doesn't change anything except the stats on the "buy" menu. What actually changes a ship's shield level or hull level?
Under 2000 it does change but above it's a diffrent story.
If you have something about 20000 it will show up in the fleet selection screen as powerful as a Sovereign, but in game it will be 10 time more powerful!
I'd take that as a: Yes it does change them. I noticed that it doesnt change them much. I added another 50 to engines on one of my ships, i got the ship going 5 MPS faster -.-