Then, when I experimentally re-named the Misc folder(So it would be ignored) with the new FSDT objects in simobjects/misc; there was no delay and obviously no GSX either.
It's normal there would be "some" delay, because GSX adds many hundreds of objects to the Simobjects\Misc folder, but it's not normal it would take so much time. I tried it just now on my system, and it takes 6 seconds with the Misc folder enabled, and 4 seconds with the Misc folder renamed. I'm using an SSD, if you aren't, it's expected you'll see a difference, but the relative timings shouldn't be very different.
Perhaps you have other folders, like a specific folder for an AI Traffic package that, put together with the Misc folder, bring the TOTAL number of objects in the Simobject folder, to an number where it takes too much time for FSX to scan for it. In that case, I guess you'll simply have to live with it.