maybe Jabo will come along and say "i didn't implement HQ_x because.." (i didn't ask) there are lots of possible reasons.
my points, which were not backed up in any way, were:
1) it won't look very good
2) it'll be even slower
try applying hq2x to some n64 textures and see what it looks like (serious question, i don't know). i was not around for this stage of pj64 development. i understand the topic is of interest to many users.
edit:
um, the way the algorithm works is highly relevant, you have to pick the right method for the right content, i know HQ series do not work well on smoothly graduated textures.
from the Hq3x page:
The filter was not designed for photographs, but for images with clear sharp edges, like line graphics or cartoon sprites. It was also designed to be fast enough to process 256x256 images in real-time.
that's *one* 256x256 image about 30 times a second. now think what an average n64 texture looks like (more like a low res photo designed for tiling, than a sprite), and how many of them there are in a typical game scene, and you start to see the problem. imho something like Rice's high res re-texturing is more the way to go with this... of course some games are 2d with cartoony sprites (paper mario perhaps?) and they might benefit from hq2x, but it's not many and will take great intelligence to apply properly in the right places (Jabo already tries to do this with Super2xSAI). another reason i'm not keen is when these "better quality than the real thing" options are implemented, users tend to just turn them on without thinking too much. (right now i bet there's lots of pj64 users out there getting worse looking games and lots of slowdown because they turned on super2xsai when they saw the option and didn't think about it again).
this is getting long but:
a lot of the problems remaining are to do with the *edges* of sprites, where they're transparent and often overlay high res parts of the scene. filtering does not help with this (actually forcing filtering is one thing that consisently makes it worse in jabo's plugin), it's a different and larger issue that should probably be tackled first imho.