Yes,
Ebbe and
Ebba are the male and female versions of the same name. :) It's not unusual for Germanic/Nordic names to have a male version ending in -e and a female counterpart ending in -a.
Inge /
Inga,
Tore /
Tora and Göte / Göta are some more common examples. And they're not pronounced the same -
Ebbe ends in an e like in "set", while
Ebba ends in an "uh" sound.
I have another batch of these ready, I'll make sure to post them soon. ;)