Short answer, yes, a permit (endorsement) is a infringement and uncostitutional. Even though the penalty is "only" $35 for not having one it is a prior restraint on the peaceful exercise of our RKBA. The permit is also a fee to exercise a enumerated right, to avoid the prior restraint, and as such it too is unconstitutional. The exercise of our right in some political subdivisions makes the crime (penalty) far more severe and as such is a infringement and unconstitutional. The state of MO continues to permit these infringements because they generate revenue for the political subdivisions...and lawyers.
As to that yelling fire thing...there is no government imposed prior restraint on you yelling fire, but the penalty for yelling fire, even in a empty theater, exists. Your 1A is not infringed so go ahead and yell fire, your freedom after the yelling is (will be) infringed.