I wear socks under my neoprene guard socks for a couple of reasons.
First, because the neoprene has a tendency to slide on my bare foot which equates to blisters or torn skin when the skin on my foot is soaked. The heavy wool sock negates that sliding.
The second reason is to keep gravel away from my foot. I don't know about the rest of the wet waders but I only wet wade wearing long, supplex nylon pants. My heavy wool socks go on my bare foot which gets pulled over the bottom of my pants legs and the neoprene guard sock goes over that. This layering keeps the gravel between the neoprene and the sock, not the neoprene & my foot.
Another reason is because I buy my wading shoes a size to a size and a half larger than my street shoe so I can wear heavy socks in winter, the only time I wear waders (meaning hippers). Wearing heavy wool socks when wet wading replicates the fit I am used to in winter.
The final reason is every brand of neoprene guard socks I've tried in the last 15 years positively suck and must be designed by & for Chinese women who bind their feet, not someone like me with large calves and thick ankles. As a result, I can barely get them on my feet and then ONLY with NO sock underneath which negates the advantages I find to WEARING socks. Simms admitted as much to me when I called to complain about their latest iteration.
Because of this I am still using two ancient pairs of the old brown Simms Guard socks that were PERFECT. However because they are old, the neoprene on the sole is compressed like heck so a sock underneath gives me some extra padding & protection.
If folks can get by with just a neoprene guard sock, more power to them but that system just doesn't work for me...