PCB input smoothing capacitor layout
I was wondering if this placement is bad or not because their position is "over" the input so maybe (unexpected?) current will "hit" the pin before being smoothed by capacitors.


For any frequency signal that an MCU input can respond to, the position of the capacitor "before" or "after" the pin does not matter. Only that it's within a few cm of the pin.

I would not change the design you have.

On the other hand, I'd avoid double-sided through hole design. Where you have your resistors located, you won't be able to inspect their solder joints after the MCU is installed. I'd move them out from under the MCU also.