Yes, more or less. Also, if they're not mechanically symmetrical, there might be a phase shift, which would be at an angle to the terminal voltage so adds up slightly different (however, it would have to be quite some angle for this to actually matter). Or harmonics due to differently shaped slots, perhaps.
How much is acceptable, is how much lost capacity you can accept. Probably 5 or 10% would be on the annoying side, both in terms of wasted efficiency as well as reduced capacity.
The shunt won't show anything different under load, given the division of currents across its resistance. (i.e. ideally you'd load both either side of the shunt equally, but if you're loading just one, obviously you'll see a bit more current through it.)
It can be removed for operation.
Tim