Depends on where that filter is. If it’s inside a file you’re importing as a layer you should get no performance hit.
I could be wrong since I got no insider knowledge here, just empirical, but for all intents and purposes file layers are like single raster layers, as if the file image was flattened - it just gets automatically updated when the source file is. Any filters inside are flattened. And if you apply a filter to the file layer itself it’s like applying one to a paint layer, not a collection of layers and filters and whatever else you got inside the original file.
File layers are really helpful for RAM-starved systems. I recently painted a cover art into 16 files + a main file combining them and applying shared effects. They’re 1.1GB on disk. Each when open takes 2 to 3 GB of RAM. Combined that’s more memory than my computer has, but the file layers made it possible to work on the main file in a non-destructive manner without having the computer halting all the time. Krita is a life saver!