The Japanese monarchy has gone through cycles of governance and non-governance, remember the shogunate? I have no reason to believe that it won't happen again 50, 100, or 200 years from now, without ever having broken the chain of succession.
The chain of succession has been broken a few times, most prominently by assassination, where the next candidate assuming the throne had, ahem, well, ample reasons to be glad they hadn't invented DNA testing yet. The unbroken succession is largely an article of faith, concocted in the late 1800s in the service of turning an often fractious bunch into a modern nation-state.
It's entirely possible. Most non-governing monarchies still have themselves inserted into a position of power and simply rubber stamp the actions of the governing bodies. In the UK the Queen (or future King) has the ability to Veto a piece of legislation. Similarly in Canada, Australia and New Zealand the Governor General holds the veto amongst the other reserve powers.
However, the Japanese Emperor has no 'reserve' powers. So its ability to take power may be more restricted, however there's always a good chance that they would be restored to power in the event of an uprising.
