Debounce Functional Clock on AM335
When it says "cells" it's simply referring to the I/O logic cells that are a part of the GPIO module. As stated in the reference (25.2.2) the GPIO modules require two clocks: the interface clock and the debounce clock. 

If you go further down to section 25.3.2.1 it describes the debounce clock: "The debouncing clock is used for the debouncing sub-module logic (without the corresponding configuration registers). This module can sample the input line and filters the input level using a programmed delay." So, it does what you'd think (as the name describes), it filters out any glitches/false positives on a GPIO that's been assigned as an input.

Go a little further and in section 25.3.4.4 it describes the debouncing time and how to calculate it and enable it on a general purpose input.

And finally I found this https://e2e.ti.com/support/arm/sitara_arm/f/791/t/217327 where someone is talking about using the debounce feature.

Hope that helps clear up the mud some.