After doing a number of optimizations, our 2000 row table took 1.2 seconds for chrome to insert the elements (purely the appendChild call). That was down from around 2.6 before trimming down the HTML.
I can click "Show All" and "Hide All" over and over and there is hardly any delay. Maybe you should upgrade to the latest and see if it makes a difference.
UPDATE: At least 3 of the culprits seem to be MutationObservers from my own extensions (as in, from extensions that I have written for myself) that have {childList: true, subtree: true}! I guess I will have to optimize them. :-)
[1] https://queue.taskcluster.net/v1/task/Uht_zkkPThu384OAHNPwdA...
Once layout is involved even without looping to set innerHTML it becomes a lot slower.