Speciation in prokaryotes is based more off then just DNA sequences. Even though yeah you have lots of DNA polymorphism within bacterial species, that one species will exhibit all the same physiology, for example they will all prefer to grow in the same microenviroment, produce a majority of the same enymes, have almost identical morphology, etc etc. Besides even if you get a point mutation in an enzyme (that would ultimatly lead to a decrease in DNA homology) that enzyme is still going to be conserved in function among the species, if it wasn't theres a good chance that bacteria might die.
I believe bacterial DNA polyermase also has a lower fidelity then Eukaryotic DNA polymerase, so more mistakes = more mutations = less homology.