There is a difference between "having a voice" and "the sound of a voice" ... since the spell does not mention anything about the ability to communicate and/or speak languages, then alter self would not in any way free a Kenku from its racial curse.
From the description of the curse:
Finally, to ensure that the kenku could never divulge any secrets, their master took away their voices.
They do not have a voice. You can't change the sound of something that does not exist.
Addendum: We're having debates in the comments about Kenkus having a voice or not, since it is kind of possible to go both ways, subjectively speaking.
I personally chose to focus on "the kenkus have had their voices removed, so they technically do not have a voice".
Others prefer to think they still have a voice, since they can mimick sounds they heard, including other beings' voices.
So in the context of that question which is about changing the sound of one's voice (alter self is the name of the spell after all) I see an additional argument to support my answer/interpretation:
- If you can only mimick sounds made by others and are unable to produce new sounds, by yourself, how would you be able to change the sounds of your mimicks ?