It has no effect really for future updates. The one in marketplace are usually scenery updates. Like more photogrammetry data, for cities, more points of interest, custom handcrafted airports that places itself on top of the default base.
If you’re getting bugs, it’s more likely coming from the system update itself that’s mandatory. And you’ll get them regardless whether you install the marketplace content or not.
Unless the bugs occur on the location of those sceneries that you have installed but nowhere else, then it’s a bug from that content.
I have everything installed myself.