Look at the 'capabilities' of your PCB manufacturing house. Mechanical drills are used for relatively large holes. Very small drills will result in a higher cost. For extreme tiny holes (like 100um) laser drilling is used, which is more expensive.
Once you have the hole size, there needs to be a minimum annular ring around the hole. Again there may be more than one possible choice of minimum with a higher price associated with a smaller ring. Sometimes the manufacturer will have a specific via minimum specified that is a bit tighter than for through-hole pads.
You may be concerned about the current capability or electrical resistance of the via, which may point to a larger size.
Creating a vast sea of functional (say not just stitching vias which will test as good even if a few are not) vias at the absolute minimum via size may affect manufacturability and the manufacturer may ask for more money or refuse the job, as (as they sometimes do when someone creates a coil at the minimum trace/spacing dimensions) because yield will suffer.
It should also be noted that usually extreme small via sizes, thin traces etc. are associated with boards with many layers (eg. HDI boards) and are generally made in a separate facility from cheap 2/4 layer boards. As such you can easily see one or two orders of magnitude price difference for a similar size board- sometimes three, depending on the quantity and what kind of pricing structure they have. So a $20 order may turn into a $1500 order because you're paying for all that capability in that facility.
Of course you can draw whatever size via you want in an EDA program like Altium (down to some extreme tiny resolution in PCB context, and Gerber files have some resolution due to the number of digits used) however there are 'Design Rules' that you generally set before beginning that will be used to check that what you are creating meets the capabilities of your selected gamut of fab houses.