The simplest way to account for these is to take the average over the area. Find the annular ring or cross sectional area of one via, multiply by the total number of vias, divide this by the total area of concern (usually the area under a device) and multiply by 400 W/mK (assumes Cu = 400 and FR4 ~ 0).
This method is a bit simplified. It doesn't account for the dielectric around vias as they pass through interem planes and it assumes the heat from the package to the board is ~uniform. Depending on what you're trying to do, you may need more refinement.
