What are the differences between ships apart from those clearly stated in stats?

One thing is obvious: maneuverability

However, are there differences in maneuverability between variations of the same ship?

After the patch, I ended up with Warthog Territorial Defender that has stats worse than its inferior variations - less armor, less capacity. No benefits, it just says it's an Assault Variation and it's the most expensive one. I can't really notice any difference in maneuverability between Warthogs myself... So what's the deal?

I had a similar situation. I solved it by selling my territorial hog, and rebuying a new one. it may have been a minor bug from switching from old ship classes to new ship classes.

Hmm, there's something a little strange, but the stats look better to me.

Warthog: Mass 6000, Armor 9000, Cargo 14
WarthogTD: Mass 5300, Armor 9700, Cargo 8

Plus it has a higher thrust and max speed.

Are these the numbers you're seeing?

Something odd about the ships I see is that the armored variant of the Valkyrie has 1000 more armor than the assault variant, when the assault variant has only 100 less mass.

valks are very light, so 100 is probably a larger percentage difference for it?

umm... Vlad
why did you compare the worst Warthog with the best one? O_o

Compare TD (the most expensive/demanding) with (cheaper) MkIV and MkIII, you will see what I mean.

"After the patch, I ended up with Warthog Territorial Defender that has stats worse than its inferior variations"

'Cause it was easiest. :) I'll look into it tomorrow.