For pre-receive hooks which are allowed to be configured at the repo level, you can set enforcement
PATCH /repos/:owner/:repo/pre-receive-hooks/:pre_receive_hook_id
{
"enforcement": "enabled"
}
Status: 200 OK
{
"id": 42,
"name": "Check Commits",
"enforcement": "enabled",
"configuration_url": "https://github.example.com/api/v3/repos/octocat/hello-world/pre-receive-hooks/42"
}