I've been thinking about the same setup for my 1/32 VIIC. The conclusion I've reached so far is to use a snorkel for air intake. Reasons:

Realistic. This is how it was done in the real submarine, and I've become interested in reproducing as exactly as possible the workings of a submarine.

Reliability. By filling the pressure tank with air in the ballast tanks, you'll only get as much air as is in the ballast tanks at the surface. Also, you'll have to figure out how to shut off the pump before non compressible liquid gets into it. With a snorkel, you can fill a pressure tank with as much air as the tank and compressor will allow. No matter how deep you go, you should have more than enough air to blow the ballast tanks.

I believe this has been done - somewhere I saw photos of a pressure tank with gauge mounted in a UK built model.

This is still in the design phase, but the first problem I encountered is the primary problem any submarine modeler deals with: space. The car air compressor I disassembled was too big to fit in the pressure hull without removing one of the batteries. Of late, I've been thinking about using an old .060 Norvel glow engine from a small model helicopter as the compressor, and driving it from a 12 v motor. Devise a valve, put it in place of the glow plug, and connect the snorkel to the carburetor hole. The snorkel valve would be interesting, small enough to fit but large enough that water surface tension wouldn't block the valve. Like I said, still mulling this one over.

Another real nutty idea that occurred to me: what about a gasoline engine for surface running and battery charging? This would probably require a larger scale, say 1/16, to accomodate the smallest engine I can find with electric start (a weed eater). That would put it at 14 feet long... but it's fun to think about. Come to think of it, the Das Boot filmmakers used a 20 foot model that seated one person, but it didn't dive. Now that would be interesting (if not provocative) on the local lake.

--John