The ones that I have work on had a place on them to put air in them I would suggest to check and make sure the valve core is out before you start welding on them.

Another thing to check is where you are welding on it....a lot of older pontoons are simply full of air and or water..(well shoot thats why they need fix lol).  But newer ones will be full of styrfoam blocks and sometimes spray foam on top of that.   That stuff makes some nasty smoke  and even nastier welds if it melts into your joint.  My advice would be to put the repair area facing striaght up if possible.  Remove the drain plug as mentioned before..drain them good....then you poke somthing in there and see if there is any foam...if its soaked wet no worries ...if its dry a little argon in there will prevent lighting it up.

Are you putting protective keels (wear strips) on them or  patching holes??  A length of 2x2 3/16 angle makes an excellent wear strip.  4043 is an appropriate rod for most boat repair.