I have this circuit that you consisted of an RC filter for a two-wire endstop, the circuit works fine but apparently they no longer manufacture single-layer 100nF capacitors, they are only found in multilayer, can I replace it?
Your schematic utilizes the capacitors as a filtering element at low frequencies. The choice of MLCC vs single-layer should make absolutely no difference as long as long as the MLCC version has the same voltage rating. MLCC capacitors can provide a slightly smaller footprint (more compact) with perhaps a slightly taller height. Unless you are operating circuits at high frequency and care about the tiny differences between MLCC and single layer caps, you can feel confident that both types are essentially interchangeable.
Here is an article discussing the differences. https://www.mwrf.com/technologies/components/article/21848633/opting-for-singlelayer-or-multilayer-capacitors