I'm actually a little surprised the pyra shows up that high. Essentially it's covered in hull, making it the easiest ship to take out with piercing/explosive combo.
But back on the junker, it doesn't make that much balance sense for a ship to have that high of armor and mobility combined with a difficult to hit hull and a large area of cover for it's guns.
Toss in a buff hammer and things get more extreme. Since they're all % based, the higher the base stat, the bigger the boost. The junker has the second best armor, acceleration, turn speed, turn acceleration, and the best vertical speed.
Certain other ships do need a bit of a boost, but it's easier to deal with one ship at a time than try to tweak the remaining ships and risk things getting more out of balance.
Although, since we're on the topic of ship balancing, the goldfish probably needs the most love. It's not used in competitive play too much (although I think a lumberfish might work well against a junker maybe), and it's not used very effectively in newer matches either. It does see a fair amount of effectiveness in some moderately experienced pub matches, but that's about it.