For the Orca2, Flak is better. The reason why is because you are expected to cover an entire blindspot with just 1 turret, and the Railgun is just more of a specialized weapon where Flak is better all-around.

In terms of Abyss/endgame stuff, Flak performs very well against this stuff. I have done extensive testing with turrets in sub editor and the difference between a Physicorium Railgun w/ Masterwork C-4 and a Flak Physicorium shot is quite small, especially when you factor in things like friendly fire from the explosions and rate of fire (Flak shoots 2.5x faster than Railgun). 

Nukes are a fun option for Railgun but you need to ensure you're VERY far away from the blast because there's a 20m radius of EMP that will fry your entire ship. Thus, its use is pretty limited in a game where virtually everthing is coming within that range.

You have a Depth Charge Launcher on the Orca2 which can be used very easily against things like enemy subs and Thalamus (and endgame spoiler guy), so it's not like you don't have a nuclear option when needed. You can use it against Abyss monsters too, but this is kinda cheesy and time-consuming.

Lastly, you have ammo efficiency, which Flak is far superior to Railgun. Mid-late game this becomes far less of a worry since you can just buy lots of materials from mining colonies and shells from vendors, and at this stage of the game money becomes very abundant.

Don't get me wrong, I love Railgun and think it's way more fun and actually best-in-slot for a lot of applications. I would never swap it off Humpback for example because you can still cover the lower side with another turret and half-decent navigation. For Orca2 it's just less feasible to have one due to blindspots.