I'm fairly sure there are clever ways around the phase shift issues for low (<24dB/o) cutoffs, but I may be wrong there. Of course, digital devices wouldn't suffer this effect unless they are modelled to do so.
Of course, there's no way around the phase shift in the EQ section, however post-eq pre-internal summing it would be possible to factor in a phase correction. I'm not sure if any EQs actually go this far, and it would certainly be harder with a PEQ than a GEQ, but not impossible.
Does anyone know of any phase-neutral (or close to it) EQs? To be totally honest I've never really researched EQs that much, my main interests lie in PCB topography and op amps (wherever they may be).