Do what makes you happy. If you think opposite direction trunks is good then go ahead and try it. You may cop some criticism from the Bonsai Police but if you are committed to doing it your way that shouldn't matter.
No problem to chop and remove one of the trunks any time of year.
If you've tried and found you don't like the look it is very easy to chop later.
Also no problem to removing some surface soil to see where the roots are at. That can be done any time of year. Any tree can cope with losing up to 10% of roots any time of year. That's actually happening all the time but we can't see it so don't understand the constant underground battle between plants and soil life - fungi infect roots, insects eat roots, digging animals cut through roots as they dig. Those things happen all year round but the plants still keep growing new roots to replace what's lost.
All that means we can dig around the trunk and even chop a few small roots any time of year without harm to the tree. Just don't go ripping the entire root ball apart in Summer.
Pruning can be done any time of year. Just be aware that junipers don't seem to like having too much foliage removed all at one time. 50% should be safe. Then let the tree recover for 3-6 months before attacking again.
Junipers can also be sensitive to bending while they are growing strongly in Spring. Strong bends can separate the bark from the wood and kill branches at that time of year. Doesn't always happen but enough to avoid Spring bending where possible. Any other time of year is usually OK.