
PC Users: Place Everywhere has a great alternative to scrap mods, if you press Insert on your keyboard it enables "Extra Object Selection" which will let you scrap everything that can be accessed in the game without disabling the Precombined data (which is the problem with those scrap mods).
Best bet is to remove them on your next play-through. If you're running into FPS issues, especially in your settlements, disabling mods like these will help quite a bit - though keep in mind that anything you scrapped while they were on will return. These types of mods function by disabling or destroying systems in the game designed to make your framerate smoother.
Mods like Scrap Everywhere and Spring Cleaning will inevitably destroy your frame rate (and possibly the navmesh). Almost all of the Sim Settlements buildings use the Fallout textures, which means that they will be updated to the very high resolution textures provided by that pack. Avoid the High Resolution Texture Pack from Bethesda. This will give you more control over how many new polygons are added to your settlement. Limit your plot count to a smaller number to start and add more slowly. While this isn't the most fun of options, it may help with stability on lower end systems, as you get to individually choose which of your plots upgrade once they are eligible so you can see what effect that building upgrade has on your frame rate. Try setting Upgrades to Manual in the Holotape options. This will reduce the amount of things your game needs to render the moment you arrive. You can build this mat under Resources > Miscellaneous. Create yourself a fast travel target that is near the edge of your settlement and facing away from it. With that in mind, here are some things you can try if you find that your frame rate drops really low or your game crashes when hanging out in settlements with a lot of Sim Settlement structures. Also, because Sim Settlements uses an upgrade system that results in your buildings creating more polygon-intensive models over time, your frame-rate may be lower after returning later on. While it allows you to get highly detailed settlements built without needing any special mods or tricks to increase your build limit, the build limit in general was designed to prevent your system from crashing. The method used by Sim Settlements to create its buildings bypasses the building limit meter for the most part, and this can be both a blessing and a curse.