Is disk speed still relevant or is it really mostly memory speed/capacity and threads? How relevant is single core speed these days?(ie how many key steps are not parallelized?)

That's gonna be highly specific to your software. Disk speed will always be important for reading data - for a closed search using Sage, reading data takes longer than searching data. FP/DiaNN/MQ all do pretty heavy disk reads and writes throughout their execution, so that will impact them more.

I use a Ryzen 2600x with a 1TB 960 Evo M.2 drive and 48 GB RAM. It finishes much faster than any of the more expensive Lab computers with Xeon processors. I keep the task manager open when running FragPipe, MQ and DIA-NN; CPU and disk speed are always limiting factors on all lab computers.