If the taproot is not hugely inconvenient, I wouldn't necessarily cut it all off, especially if that's where most of the new feeder roots are growing from. What I would do is cut part of it now, and maybe the rest next time you repot. It's just safer. Don't be TOO careful though, at least 1/3 or so can be taken, if not 1/2, because you need to encourage roots to grow from above in a wider area. Teas like high humidity (but from a wide tray of stones, or room machine rather than spraying), very high light (i.e. full spectrum fluorescents 5-6 Inches above it for 15 hours a day, and if your mix does have a lot of grit in it for fast drainage (a good thing), water when no more than the top 1/4" has dried, but not if you're trying to grow it in potting soil full of peat that never dries (at the roots anyhow) and can rot roots, though the tree will suffer as it should be in bonsai soil so it can be kept moist (NOT 'wet') throughout.

I would wait some time (even years) before necessarily doing that as Fukien tea (unlike e.g. maples or pines) does need a little more water in the soil, and if you have a young tree in a very(!) shallow pot, you're going to end up having to water twice a day even indoors, and that's asking for other problems. Once it's more established, with a larger trunk, and the roots have been worked over several years, then I would consider it.

Remove the moss. Make sure the pots are up on pebbles or something in those trays because they may well be wicking water up to the roots, effectively drowning them (and you're probably watering too often anyhow, except maybe for the Fukien tea). To provide more humidity, trays must be much wider than pots - regular saucers are only to catch 'watering' water. Yellow leaves does usually mean things are too wet, so back off the frequency and let some of the soil dry between waterings. Junipers are outdoor trees, even in Canada, providing they have proper winter protection, so while it's too late now to put yours outside - it'll be shocked by the weather as it didn't go dormant in Nov. thru now gradually - if it's still alive in Oct. I hope you'll have researched how to take care of it then and have somewhere outside to put it. Do put all out in May if at all possible... and I know what you said, but that's why it's a bad idea to buy them before researching. If those pebbles are glued down, get them off entirely so you can see what's going on with the soil... There's no room here for an instant course in bonsai, never mind for 3 trees, so you'll have to do some learning on your own, though whether or not the trees will wait is another story. Very high light is extremely important for those trees, and you need to look at special fluorescents (not just "gro lites") for many hours a day right over their tops or they won't do well at all. Go look at Bonsai4me.com, look at www.bonsaihunk.com, evergreengardenworks.com for starters, and then go to http://ibonsaiclub.forumotion.com (terrific forum with experts and much more activity than here).

It doesn't seem to be in need of being re-potted. I am wondering if it is just over watering that is causing the leaf loss. I have been reading that these really do like the soil to dry out between waterings, not just the top layer, although it hadn't been an issue until recently. Nothing else has really changed that I can think of. It has been sitting in the same place and was happy there just a few weeks ago.