HI Akos,
Welcome to the forum. A few answers to start you off - there are several ways of doing things and I'm sure you will get many more responses.
VW doesn't care whether the hole was drilled, cast, punched etc. There may be a 3rd party Drilling Plugin but otherwise VW will faithfully represent a void of the shape you define in the location you define.
One way of doing this is indeed the solid subtraction:
Model your drill bit's effective shape, including taper angle etc.
Save it as a symbol with the point set to the insertion point.
You can then position the symbol as required over and
over, perform Subtractions and even replace this bit with a
different on if needed by using the Replace button in the
Object Info Palette.
3D constraints: There is no 3d dimensioning in VW (yet). It has been on the wish list
for a long time so there are effectively no 3d constraints available either.
There is however a robust 3d working plane system and the Align Plane mode of the Working Plane tool helps achieve accuracy in 3d.
3d snapping works effectively as you will have already noticed.
History: A solid object contains a history of all the operations that went into it's creation.
There isn't a visual history but by double clicking it you can view the previous
steps and all it's generating objects. At some point this may become unwieldy
whereupon you may decide to do away with the history by
Modify>Convert>Convert to Generic Solid.
Spring: There are built-in 2d and 3d spring objects in the Machine Design : Tool Sets Palette.