Using two at once should work fine! Each VTubeStudio instance will listen to a different port, so if you open the control panel twice and connect each instance to the corresponding VTS port (which can be checked in the VTS options), you can control both displays independently.

The timer doesn't currently have pause functionality, but I can add it! I've opened an issue to track development on that, so it'll be easy to track progress and see when it's added:
https://github.com/Renpona/VTS-Clock-Standalone/issues/1

Ooh, this might be nice for a countdown clock for some launch streams where they cut out the clock. And in the case of ULA launches, they have two timers, the L-minus and T-minus clocks, the L-minus runs continuously, whereas the T-minus gets stopped during planned hold during the countdown. Is it possible to use two of these for that purpose?