It's more the pain in the hips that's the concern atm and it's possible that this has been contributing to the knee clicks and whatnot. However that does not necessarily mean that sumo has been the cause, as it could have also been a technique issue high bar squatting that has caused the hip issue and that has carried over. I might stop sumo for a while to see if things improve because things aren't feeling too brilliant today (better than last night though).
Doesn't sound pleasant, and sorry to hear it.
The issue may well be caused by the "knees out" cue, which caused me huge problems with my squatting. If you don't use it then ignore.
I found that as soon as I stopped trying for "knees out" and both feet parallel, etc., my knees and hips stopped hurting and I could squat a lot more (and my legs and glutes suddenly became even bigger... Which wreaked havoc in other areas). And no, my back didn't suddenly explode, and neither did my knees. Aaaaaaaanyway.
You are experienced enough a lifter to work out what works for YOU and your own quirks/skeletal structure, etc. so if something works for you and you lift more doing it, who cares what other people are doing?