GSX is disabled while cruising, but "disabled" only means it won't try to look for airports around you in case you need to pre-select a gate when still in flight, but that doesn't mean it's totally and entirely turned off.
Of course, it must still check, at very low update intervals (ever 4 seconds, which is the lowest Simconnect allows), when you are starting your descent so, basically, it will still check your altitude and airspeed, but that's about it.
1-3% of your CPU cycles is nothing and it's entirely normal (I'm sure you have lots of other processes running taking more cycles) and, under DEFAULT conditions, the OS should take these cycles from a spare core of the CPU, so normally you shouldn't be able to see any impact of GSX, just because it's running.
However, if you played with the AffinityMask settings, overriding what the OS is doing to handle spare CPU cycles, it's possible you are working against the OS so, the first thing to try is to remove any tweak to the AffinityMask and use all default.
And, if you have Hyper-Threading enabled, try to disable it in the BIOS, because all reports seems to indicate P3D works more smoothly when HT is disabled.