Hey Shelf,
Welcome aboard. As stated by others you can just ignore them and continue on to your grid. What I like to do is dive to 20 meters, go to all stop on the engines. Then I right click on the hydrophone operator and do a manuel sweep on sound. If you pick him up chances are you won't have to chase him too far.
no refueling available in vanilla mode. After you have enjiyed stock SH3, try the GWX mod. It will blow you away..............