Hello,
The number of applications running won't affect the Bluetooth connectivity of the Apple Magic Mouse. The normal cause for Bluetooth connectivity issues with an Apple Magic Mouse are low battery charge or some form of interference.
Bluetooth uses the 2.4GHz radio frequency, which is also used by Wi-Fi, microwaves, and fluorescent lighting. If your Wi-Fi router is close to your Mac, try moving it to another part of the room if possible. Same goes for any fluorescent lights.
See if that helps,
C