As a JV coach I encourage my MS club players to go to club practice when there is a conflict. Typically training level is higher and its in the players best interest to go where the training level is higher.
It only causes issues if the coach allows it to cause issues. Be honest with the other players (and parents) and be consistent and thats all most reasonable people ask. I feel like so long as they are training they are getting better. If they are getting better they will play better for me.
I don't know of anyone who honestly believes that JV is commensurate to a good club team. Level of play at even the best JV teams simply isn't equivalent
Are there softer benefits to playing JV.....of course!!! But from a soccer perspective make sure your coach will support your son/daughter when there are conflicts and there will be conflicts. If the coach won't.....play club.