This is a known issue/behavior when having the Managed Build System enabled. I've seen along the time several issues logged against CDT with similar description. One example I quickly found is [1].
You could adapt some settings, depending on what you want to accomplish. You can explicitly disable auto-build inside launch configurations and make sure to manually build the project, when needed. You also have the option to disable Makefile generation inside build configurations, but this is risky from a development perspective if your project relies on this - you'll have to manually reenable when source files are added and you won't be able to change any build attribute.
Unfortunately, there's not much what we can do on MCUXpresso IDE side. The slowdown is generated by CDT's Managed Build System implementation and reworking it at this point is not feasible.
Regards,
MCUXpresso IDE Support
[1] https://bugs.eclipse.org/bugs/show_bug.cgi?id=223815