HTLs just round main station=HBF tend to be overpriced and not with best of service-but thats marginal. On a site like booking.com one can compare all factors, also on a map. The german equiv. of booking is hrs.de-but they tend to offer much the sameness.
As about anywhere in DE in a big city public transport is good-best are the railway-run S-Bahn, and these also start much earlier as the tipical /en/-man is used to-think around 5.00 a.m. Around 6.00 in HBF is already near peak time.
I for myself often stay in hotel BB chain-most of these are very near the big stations (but not in MUC), basic and good value, for some perhaps too basic. They only offer BF for meals-german style.
IF you want a hint of I know it from UK: seek for Premier HTL-now also around 50 places in DE-and the same reliable stndd as in GB-incl. the brekkie. Prices very variable with demand. In fact I am right now on my way to stay in one-in another place.
It seems you have booked already-for others; WestBahn, the private competitor to OeBB now also has 2 trips/day from MUC-via their core route: Salzburg-Linz-Wien.