You can say "a" in Hindi; it's "ek" and it means "one." Though often, Hindi speakers omit that.
If you say "चूहा काला होता है" it means "a rat is black." As in, rats are black, generally. It's the habitual; rats have a habit of being black. Take a rat - it's black.
" चूहा काला है " can either mean "the rat is black" or "a rat is black." If it means the second, it means "a certain rat is black."
होता can't be translated, but its presence means "can be" or "usually" or something like that. Just think of it as a way to generalize.
You typically wouldn't use it in a sentence like here though; you would say "rats are black" if you were talking about all rats. But if you are using it with a singular it is synonymous with "a rat is black."
Source: grew up with a Hindi speaking Nepali nanny.