Perhaps everyone getting launched from the hecate hull was due to magnetizing that area of the ship to make the herc 2's stick until they are released. As for the long sensor booms on ships such as the herc 2 and perseus, those are most likely retractable. The fact that we see something like a perseus inside the main hall with it's sensor boom sticking out and jutting into the floor is probably on account of V thinking that most people won't notice and they didn't want to remodel the ship to have a retracted sensor boom.
Another thing is that V stated that the ships in fs are anti-gravity capable (they can hover around like a herrier if they want to). This obviously puts a different spin on how the ships can take off. But from what we see in the psamtik main hall is that the vasudans seem to have a system like bsg has for launching ships. Except for the vasudans it works for both taking off and landing, and taking off happens from the ship firing up it's engines. In bsg when the fighters get launched, it's not based on their engines getting up to speed. And landing the craft takes place in a whole different area of the ship.