Visually this thing is gorgeous, lovely departure from the grey greebleboxes. Interior does a lot with the space (I have no idea how you managed this much on such a small ship) logic works well for the most part, didn't have any glaring trouble.
This might just be preference but i always hate this door setup since the door doesn't close if you run up to it and back off, and the whole thing is a disaster with multiple people running around. I prefer to use one detection area on both size; connected to a series of delay blocks; then all delay blocks connected to an or block, then the or block controlling the door. That way the door opens when someone approaches and stays open for as long as the delay series determines, think it would help a lot since interior is quite cramped.
I don't have much to contribute here since most of the ship is well above my level aesthetically, looking forward to fleet submission
Systems
Unfortunately all that advanced armor is dragging your ship down hard; Ship is too slow to flank larger ships and lacks ion effect for defense, both of which would be much easier fitted without all the mass dragging it down. Maybe swapping engine boxes and wingtops for hull wouldn't ruin exterior too badly?
Main guns are good, nice to see swarmers aren't 100% slave so they can actually chase.
Top turrets are lacking; they are too weak to go through hull blocks and even some system blocks: not good. Consider swapping slave for pulse so they can hit interior, or converting to ams since the ship is lacking that completely.
The medium turrets are ok but would benefit from punchthrough slave more than overdrive i think
Overall very nice build!
The detection blocks for the doors are best for solo-play, that is true. I've seen the delay block system and that too has its faults, but I'll take another look at it.
The faction thread implies that the combat capabilities of these faction ships should be reduced in favor of better interiors. Having faction ships be weaker than player-made ships is also sort of necessary from a gaming perspective in my opinion. As such, the decision to make the Hydra slower was a conscious decision based on that fact--players in small fighters should be able to run away if they realize they can't match the Hydra's shields and firepower.
As for the firepower itself, the top turrets are small and not intended to be powerful. The medium turrets I believe are Piercing, but you are right, Punch-Through might work better.