Yep, the SH4 rearm procedure will ONLY refill your torpedo reserve stock, and won't actually put anything into empty tubes. The procedure is to re-arm, manually reload your tubes from fresh stock, then re-arm once again before leaving. Note that you don't have to wait for your tubes to FULLY reload, as soon as you order the reload by dragging one of your fish from the stock into the tube, it will disappear from your reserves. As long as you have at least the transparent torpedo image in the tube that signifies the tube is being loaded, you're fine to finish up your refit and continue your patrol; the tubes will almost always finish reloading by the time you establish a hostile contact.
