1. Never used them (prefere the 25% sized ones), but I would assume they use the "maintenace facility reload time". If not, use the ammo-management tab and put the missiles in after the appropriate time has passed.
2. Not using auto-assign.
Seriously, though, you can assign a priority number to each design. Aurora will put officers into spots with the highest priority first. If, however, there are still officers left after putting one on any other ship, well, I don´t think there is a "do not assign any officer" button on the design screen (put forth a suggestion in the suggestion board)
3. Allready answered
4. Not only is there a sensor delay, but also a weapons delay, so no, you can´t shoot a missile with onboard sensor to circumvent the effects of jumping