Creating repository via Conduit API method repository.create does not spawn PhabricatorSearchWorker task which responsible for adding record to uri *_repository.repository_index table.
Because of that, it is impossible retrieve repositories by remoteURIs via repository.query API method.
Creating repository via Diffusion form - does.
I'm just going to merge this into T10337, which discusses providing modern endpoints. repository.create is a broken mess and we tend to replace it rather than fixing it (it can't reasonably be fixed without breaking the API, anyway, so we'd end up with a new endpoint in effect, regardless). The new diffusion.edit will fix this and the many other problems with repository.create.
T10699 is a similar recent discussion of another issue, and describes some possible workarounds until we fix the API.
Generally, making any transaction-oriented edit to the repository should trigger a reindex. I think there's no convenient way to do that via the API today, although you can via the CLI with bin/repository edit.