Will it have pilot-controlled weapons? Will both big manned turrets be able to link to the pilot via computer blades if the crew gets sick?

The pilot will have access to the torpedoes, and some of the other bridge stations will be able to control weapons. Like other ships with manned turrets, they're designed to be human-operated. However, as a fallback, they will be able to be NPC-crewed or equipped with a computer blade.