This is a key point but there is also the issue that most smaller ships were special craft with specific duties that the game doesn't fully simulate. For example, the Flower class corvette, probably the prolific smaller ship, was a dedicate convoy escort. It was in game terms a small slow destroyer - single gun, asdic, radar, depth charges, sometimes light AA. The only thing the game doesn't support is building a slow destroyer with exactly the right range for convoy escort work and it is telling the whole range of this type of vessel really weren't destroyers; they were based on long range fishing hulls (and their engines) without the usual destroyer 'designed for speed'. This was job that normal destroyers had difficulty with as the requirement was to be able to sail with a convoy from one side of the atlantic to the other. Regular destroyers couldn't do that but the in game convoy escort mission doesn't require it. However, the convoy escort mission does require ships to have sufficient range to reach the zone covered and that might require a better ship where an old destroyer with a slower long range engine would suffice.
There are a whole bunch of other missions for these small vessels such as coastal patrol, short range minelaying and sweeping, coastal naval dominance and things like that. Things could be added to the game to represent stuff like this but the underlying issue isn't lack of the ships types being in the game, it is lack of game mechanisms to simulate what they did. Just on the mine warfare front you would have to add a whole range of complexity about exactly where mines were being laid if you wanted to introduce the small vessels involved.