Hardpoints are made as dummy objects on the ship. If you do not use hardpoints, all weapons fire will come from and hit the center of the ship. You don't "need" them to play the model in game.
As O'Neal said, for SFCIII HP1 through HP24 are where the weapons fire origninates. HP1 through HP11 are for primary weapons (phasers), and HP12 through HP24 are for heavy weapons. The primary and heavy weapons designations are reversed for SFC, SFCII, and SFCOP. To get a good idea of where to put the hardpoints, you will want to consider the archs listed in the defaultCore file. Of course you want to to place theses on your ship where you can see the phaser strips and photon tubes.
Hardpoints A1, A2, . . . . F2, F3 are where your ship will be hit with weapons fire. I think that it was Atheorhaven that once posted how to properly place these on a model. They should be ordered starting from the bow and working counter clockwise around the ship toward the port then to the stern then starboard and back to the bow.
Bow Port: A1, A2, A3
Along the Port side: B1, B2, B3
Stern Port: C1, C2, C3
Stern Starboard: D1, D2, D3
Along the Starboard side: E1, E2, E3
Bow Starboard: F1, F2, F3
This order tells the game which side is which to make weapon routing more realistic. So, if an enemy ship is on the port side of your ship, it will always fire and hit the closest of the "B" series. If it is to the aft of your ship it will hit the closest of the "C" or "D" series.
In terms of application, you do NOT need to assign any vertexes or meshes to any of the hardpoints (or joints as Milkshape calls them). You do not need to have them connected either (like you do in Armada). To ensure that they are not connected, make sure that no other hardpoint (joint) is selected when you make a new one.
Also, consider that the Milkshape *.mod exporter flips the mesh and the hardpoints, so, you either have to build the hardpoints on the opposite side, or with the hardpoints showing, select all and then use the mirror all tool before exporting.
Because I usually just use loadouts from stock ships, I cheat by importing a stock game model for the loadout I am planning to use, deleting the stock mesh, and then merging my new ship. That way I am sure that the hardpoints will be on the correct side and that I have not missed any.