No, separate meshes dont mean more polygons
. If you have two cubes, one smaller than the other, with the smaller one placed directly beside one of the faces of the larger cube, (bare with me now, this is a really dumbed down example), if you keep these as two meshes you have a total of 12 polygons (6 per cube). If you wanted to join the smaller cube to the bigger one as one mesh, you'd now have 14 polygons (as you'd need 4 polygons on the face of the cube you're attaching the smaller cube to). Take this example and scale it up to something realistic like a character or other polygon-hog, and you'll realize more polygons are needed for the combining of the mesh. They can also tend to screw up your edge loop flow.
With that said, Im not saying you should use multiple meshes. The reason they can be slower than a single mesh is because they are different limbs, and each limb has to hold it's own data. So multiple meshes mean more limb data than necessary.
Its finding an equal balance thats important. If you're making a big factory, and you want to attach a large mechanical wheel to the side of the building, the amount of polygons you're going to need to join the meshes outweighs the small amount of loading time required to get the extra limb data in. If, on the other hand, you're giving a weapon a bunch of notched out grooves on the side, its probably better to go ahead and model this detail in instead of throwing in 10 or 20 notch models in a straight line.
In terms of the clothing question, I've only rigged / animated clothing once, but from what I know / my experience in modelling in general, I would imagine it'd be easier to rig the clothing if it were a separate mesh, as you'll run into less conflicts where two joints touch like the shoulders. It'll also make your life easier down the line if you do ever want to remove the clothing or sub it out for a newer version without having to remodel 80% of your character again.
