Torpedoes for this purpose have been replaced my missiles because missiles are WAY, WAY better at letting a small boat endanger (or sink) a big ship. For starters missiles also have an advantage in that they can be used from much father away, making it less likely that boat they’re being launched from will be shot at in return.
Also, there isn’t a price advantage like you think. A smallish anti-ship missile (i.e. something similar to what the Ukrainians used recently to sink that Russian cruiser) is going to be roughly the same cost as a smaller modern torpedo. A bigger missile is going to be comparable to a bigger torpedo.
Basically the modern equivalent of a PT boat is something like the [Osa-Class Missile boat](https://en.wikipedia.org/wiki/Osa-class_missile_boat).
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