It's really not as simple as a rule of thumb - there are a lot of factors in each application. I'm going to assume that your bolt application is a fairly traditional situation where you are bolting one piece of material to another (one shear plane) not a more complex sandwich (Isolation pads, transition plates, etc.)
In most bolted connections, the bolts are intended to provide a clamping force normal to the faying surfaces to allow a large friction force to develop between the two materials being bolted. As such, while we pretty much always check that the bolts can hold the load in shear, for design of the connection for performance, the clamping action is a greater consideration. If your faying surfaces are very flat and clean, and your two materials are very stiff, you can imagine that a single, large bolt would suffice for any problem as the clamping force would apply equal friction across the entire faying surface. One problem with using a single bolt is that if the joint does slip, it could slip in a direction that loosens the nut against the bolt, leading to a catastrophic failure.
In reality, usually our two surfaces are somewhat flexible, dirty, and not flat. Because of this, a bolt only successfully applies a clamping force for a small area around itself, so joints that resist a moment (like most motor mounts) will not be very effective with a single bolt. Instead, adding more bolts, farther apart from each other, creates 'moment couples' where because of the distance between each bolt, the actual slip resistance required at each bolt is less. In general, for connections resisting a moment, you want to maximize the overall size of the bolt pattern within reason.
There are, of course, a bunch of other factors. As you suggest, since the absolute tolerance is larger on larger bolts, they do generally require more sloppy holes, meaning they won't inherently provide alignment that is as good as smaller bolts. However, if you align your components independently (by measuring or with a jig,) and tighten the bolts, you can still keep the component in the right place just as well. Conversely, because holes for smaller bolts generally are less oversized, aligning a pattern of many small bolts requires much more precise machining of your parts than aligning a couple of larger bolts. This is because of the smaller oversizing factor primarily, but is compounded by the fact that the more holes you have, the more likely your worst case is to happen (where two holes are just within tolerance in the opposite directions of each other.) Of course, you could drill unusually oversized holes for smaller bolts, but you would find that the head (and/or washer) would not have very much contact with the base material.
As far as cost, for modestly sized parts the costs of machining the parts almost certainly costs more than the cost of the fasteners themselves, so a few larger bolts would be a better option - slightly more expensive bolts, but fewer holes to drill. The size of a hole to drill has much less impact on cost than the time to locate a new hole, especially if it deep enough to require multiple steps (like a spotting drill or center drill) and therefore a tool change. In addition, depending on your scale, materials, and thickness, sometimes smaller holes are actually more expensive as they have to be drilled less aggressively to avoid tool breakage. Two big exceptions to this statement would be if your pieces are being mass produced by casting, injection molding, or a similar volumetric process, or if they are being cut by a profiling process like waterjet or laser cutting, where linear inches are the main driver of cost. AS you point out, the time to assemble the device is mostly governed by the number of bolts rather than their size - for a given length of thread - a large bolt is actually faster to tighten. So this also favors fewer, larger bolts.
As for a formula governing the clamping force, it's nothing too special. Once you establish the pretension on each bolt as installed, you simply multiply that by the static coefficient of friction for your faying surface combination. The hard part is establishing the pretension that you will accomplish in each bolt - there are formulas that will give you tension as a function of torque, lead angle, and materials, but they are known not to be very accurate. The best way to find this value would be by direct measurement after tightening the bolts using the same method you will use in production (torque, feel, turn-of-the-nut, etc.)
