You don't need low pass filtering on an encoder switch like this, in general you don't get both contacts bouncing at the same time so any microcontroller sampling of the signals sees a valid quadrature signal. And even if you do occasionally who cares, its an encoder switch, its relative, not absolute. Just don't sample it too fast and any uncorrected bouncing issues will be limited in effect.
Actually, the exact opposite of everything you said is true.
These encoders (example a Bourns PEC11) are very noisy when switching (look at them on a scope).
A resistor and a capacitor on each pin is trivial to ease the burden on the software.
And unless you're willing to accept turning the encoder very slowly, you will want
a pretty fast sample rate. I sample mine at 500Hz to provide an expected response.
It's been some time since I've looked at these, but you certainly want to be above 100Hz.
As I said earlier, no filter, a slow update and you will often get a response in the opposite
direction than you're turning encoder. Unless you want to drop big bucks on an optical encoder.