I can’t speak to the multiple CPU question.
I think the CPU clock speed is important to a snappy desktop experience. Higher is better. Xeons over 3ghz are rare, at least the affordable E5-26XX are. The caveat to high clocks with high cores is heat. You need good cooling for a 160W CPU like the E5-2687w
Xeons are designed for server stability and not high clock speeds and not usually overclock-able, with exception of E5-16XX v3, which has unlocked multiplier but is limited to 8 cores. I have tried another 12 core Xeon CPU on the X99 platform with 2.2ghz clock speed and the experience was sluggish.
From what I have gathered, hardware graphics becomes a security risk when you pass it through to HVM. I don’t do that.
Both my systems have NVME m.2 ssd. and I prefer them to the sata ssd. I have used Sata SSD and it seams less snappy.