The tube is where excess oil sucked out of the sump into the air box is drained out. The plug is presumably to make it more environmentally friendly and to keep you from sucking anything back into the airbox (water during a stream crossing if the engine stalls, etc.).
You need to drain it. When you do the odor will tell you why it is often called the puke tube.
You have a fair amount of rust in the 2nd picture. I try to remember to do frame touchups with a spray paint that has primer included. That way I just scrub the area the best I can and spray it.
This shows frame touchup on the subframe after welding: