Yes, you will have two independent copies of GSX, which can be also independently uninstalled from the Windows Control Panel. It's the same as when installing into FSX and P3D on the same system.
Activation it's not an issue: as long as you install on the same PC and under the same Windows installation, only 1 activation will be used, regardless how many copies of GSX you install. And, you only need to activate in one sim, which means, if it's already active, it will appear as active in all the other installations too.
