AusBonsai

Just received my Japanese Maple seedlings from Shibui today... Very excited...!!!
I know that you can pretty much cut roots back to stumps on a trident maples but not sure if you can do the same with JM's. The micro's are going to be put through metal plates so all good (don't need to reduce roots/leave as is). The larger ones i think I'll have to prune back....just not sure how much to safely take off, & should the ones with longer tap roots be reduced gradually over a couple of seasons, or can the tap roots just be lopped off...?

Just lop the tap roots off. As long as its at the right time of year - ie when they're dormant before bud burst you should be fine.

Shibui recommends being a little less aggressive with Japanese maples.
Maybe also wait a little closer to spring if you want to be more careful.

Shibui recommends being a little less aggressive with Japanese maples.

but only a little less. When you see what I leave on a trident you'll realise that 'a little less ' means more than most people will willingly cut off in one go.
Even the larger maples you have are just sticks. They only need a few roots to sustain them while they grow new roots. Being relatively young and vigorous they should recover far better than an older tree as well.
If they have 1 or 2 reasonable lateral roots I'd cut below those. For any that don't have any reasonable laterals just shorten the vertical root and see what you get next year.
Most of those were just a single, untapered trunk so take the opportunity to shorten the trunks as well. I usually aim my first cut to the level I'm planning the first branch or change of angle in the finished tree so quite low.