After your wife gains Thai citizenship (and passport), to be here with full citizenship status she will have to leave on her German passport and return on her Thai passport. This can only be done by air.
In the meantime, it’s no problem. Her citizenship gives her the right to unlimited annual extensions to the visa that she entered on.
I think she might have to do 90 day reports and TM30 as well. I cannot remember.
I'm not totally wrong. That policy is mentioned on the Hull(UK) embassy site (for example), and several oil rig workers reported being refused entry for that reason (as they tried to enter once every six weeks, based on their work shift schedule.)
It is not a regulation set in stone; it is a policy interpretation of a regulation that allows them to bar entry for various ill-defined reasons .. most often applied at Bangkok airports.