1) It is a bit otherwise. CFIFO has depth of 4 entries, but Cqueue can have any length because commands are continuously filled by DMA.

Special case is using of streaming mode that can be typically used without DMA for command filling as they can be locked in CFIFO, but in this case CFIFO can be lengthened to 8 entries.
Typical issue that can lead in eQADC command underflow or result overflow is heavy loaded transfers over XBAR ports (typically SRAM and PBRIDGE where eQADC resides). Of course, if DMA is configured properly. It is needed to utilize cross-bar switch advantages and set higher priority for DMA than CPU.
2) ADC clock is 33MHz at most. In case you are using higher frequency, module may not work properly and ADC specification is not met. It is use out of specification.