Err, yes, you are correct. MUC escaped me for some reason.
Berlin, for some obvious reason, prefer to be seen as "BER" rather than SXF, TXL and SXF (the statistics published by ADV always start with the total figure for the three airports). Taken together, "BER" is third ahead of DUS and HAM.
If you just look at TXL, the next biggest airport paxwise would be, by the way, CGN, not STR...
All in all, the five biggest German airports now have LCY routes.
Out of the TOP15 German airports, 5 still have a LCY route and 7 have had at some point in the past: In addition to FRA, BER, MUC, DUS ans HAM which are still served there have been services to CGN, STR, NUE, LEJ, BRE, DTM, FMO. The only notable exception (other than HHN, of course) is HAJ which is the 7th largest airport but, to the best of my knowledge, has never had a LCY service. The other one missing is DRS, by the way.