Our company has approximately 2500 devices that we want to protect with Endpoint Protection 12.1. These devices are shared equally between 2 locations. Does the division between the 2 sites influence the licensing?

No, the number of sites of a company has no effect when installing or licensing Endpoint Protection. If you have purchased a license for, for example, 200 seats, you can also split them into 2 locations with 100 seats each.

Source: Official Symantec Website (https://support.symantec.com/en_US/article.HOWTO80852.html), Stand 06.07.2016