Well it makes sense when you break it down. They were small, it would have been handy to test them in various situations so better a mobile launch platform (what better way to transport them anyway), they were for military use so secrecy would have been important during testing (ships are easier to perform sensitive activities from than docks), and they had to be retrieved after sinkings and other failures during testing.
To be honest I can't find anything solid to say it, but it makes sense in those respects and speculating is fun.
Early military submarines were operated by man-power. Hand cranked or pedalled to provide propulsion. First successfully used to tow a mine into an enemy ship after passing under it, during the American civil war I think.
Edit: No, I take that back, it rammed a barbed torpedo into the hull of the steamship which was sunk by it. I know the towed mine method was used, but I'm not sure if successfully. It was the H.L. Hunley.
I didn't put a timeframe on it. Military submarines, experimental or otherwise, were manpowered in the 19th century and may or may not have been launched from ships. If so, could that be a reason they're still referred to as boats regardless of their size?
I proposed it as a possible reason, to see if anyone knew anything about it or had an alternative reason. You and I simply branched into a discussion about the possibility and practicalities of them being launched from ships and it circled back to the original point.
Early submarines were more like boats than ships in having limited size and range. The name stuck although of course they later become deep water, long cruising radius vessels of substantial size.