Yes, to make things absolutely tidy you would need to remove NIF Online if you are no longer using them as your tax rep.
How to do it:
a) You pay NIF Online around EUR39.90 and they will do it for you (i.e. will retract themselves)
b) You do it yourself following instructions found on bordr.
Please note that instruction suggests the change of your residence address to PT as a requirement - but this is no longer required since this summer as we know from this thread.
But I actually don’t know what would happen if you take a ‘do nothing’ option.
Because yes, NIFOnline are listed as your tax rep while they are not (no longer your rep), but you will anyway receive online notifications directly from Portal das Financas as you already subscribed to them. I have just received mine by email to pay IMI, so it’s working.