There should have been a link on the "Some replies below your chosen depth have not been shown" text, which brings you to User Settings, where you can set your Replies Header Depth and Replies Body Depth to a larger value.

Thanks, I did find that eventually and changed the value from 10 to 40, perhaps this will do the trick.

I still think it is worth considering on-demand paragraph collapse and expansion, ala slashdot, although I lack insight into how much effort this would involve, or how well others would receive this as a suggestion.

It would be a welcome improvement, but frankly, I have learned to live with the... well... peculiar way the perlmonks site works and don't mind it much anymore. Accepting literal line breaks in posts instead of br and p tags would be much higher on my ui priority list than better reply hide/show, as would dozens of other changes.
To be honest, some improvements in uptime and loading speeds would be even more welcome. Perlmonks is by far the slowest-loading website I have ever used, which is quite remarkable given that it's a text-only site with absolutely minuscule amounts of data per page. It also seems to be down a lot, too, but that impression may just be caused by loading times over a minute... after waiting 30 seconds or so for a text page to load, I tend to lose my patience and close the tab.

I already use on-demand reply level expansion, by clicking on a reply that only has the heading shown or the heading of the last reply whose body is shown.

- tye        

If you want your browser to grab all the subthreads and only show you a portion of them, there is some CSS you can use to do that. As for me, if I'm interested enough to read more than about eight layers deep, I have no problem loading a new page.