Coincidentally, after many years with the esp8266 and esp32, I just used the PCNT hardware in the esp32 last weekend.
I tested it by counting my GPSDO's 10Mhz output through a TLV3501, catching the overflow/reset on a 25,000 count with an interrupt handler, 40 times a second.
As far as I can tell it does not miss a single count. I need more hardware to verify less than about 10 missing.
Im I pretty sure you should be abled to track an encoder with two PCNT channels.
This said, I have some hardware that generates about 20,000 interrupts per second in the esp32, again, as far as I can see, (and much better verified), it does not miss any.