Thanks for the updat.e
I have the same problem and a similar setup (root mounted on SSD, /home and /var mounted on HDD, and /tmp mounted on RAM). I do have /tmp mounted as tmpfs, and it isn't commented, and I can confirm when running "mount" that /tmp is indeed mounted as tmpfs, and not on the SSD.
However, every now and then (but not always), "Reading package lists" will take several minutes. I notice the same kind of behaviour also sometimes when saving the machine state of my VirtualBox Windows machine. Sometimes it takes well over 5 minutes. However, restoring it always goes within a few seconds.
Any other idea? (Or maybe I should start a new thread for this.)