1: The port must be a bigger one, if there is a bunker you should at least be able to refit fuel, if you get the yellow anchor symbol you can also dock for a complete re-supply, but this will take you days away from your next patrol.
2: Yes, but if it's a small one chances are you cannot refit; try to memorize the ones you can
3: Yes, most likely, that's why I asked you to memorize them...
Some ports will have a re-suply ship anchored at it allowing you to resupply weapons and fuel, although you cannot dock (or do I confuse it with SH3+WAC ??).