Audiophiles are interested in high fidelity audio reproduction and are essentially pursuing a neutral, accurate sound.
The serious ones research beforehand in order to procure a system that is as close to neutral as possible, eliminating many variables in terms of the necessity of equalization. Ideally, properly designed audio equipment would not interfere with the signal; it would transmit it as is, with no alteration or distortion. This is easier said than done, of course. You must inevitably compensate for variations (resulting from faults in the equipment or intentional coloration, depending on your preferred perspective) deviating from the ideal of perfect sound, and this is where EQ comes in.
As you pointed out, software EQ can negatively interfere with the signal, reducing sound quality in the process...but so does hardware EQ, albeit apparently to a lesser extent.
While it's a better idea to use "neutral" gear along with software for any EQ you desire than it is to use "colored" gear that intrinsically colors the sound due to its design (which limits your control from the onset)...what you seem to be proposing is "neutral" gear that gives you the option of onboard EQ.
The main reason I can think of that advanced hardware EQ is not readily available in audiophile equipment is due to its complexity. It would likely be difficult and expensive to implement. Avid EQ users don't want a few basic bass/mid/treble controls, after all. Can integrated hardware EQ match the functionality of software outside of a studio setting? I have yet to see it...and judging from all the switches, knobs, and tricky circuitry that would be involved, I may not want to.
That being said, I would be interested in a desktop device dedicated to EQ (with corresponding graphic/parametric visual interface), as long as it is more effective than the alternatives. I believe that separating it from the rest of the chain would be a more elegant solution than worrying about how to integrate it into another component.
In a nutshell: Let the amps and DACs do their job. Add an EQ box to do it right. At least that's my idea.