Yes, you’re right, Jira allows you to create up to 100 webhooks for a given site.
The warning, in the other hand, mentions there may be some instability when having more than 50 active webhooks. The rationale behind that is that webhook communication (traffic) is not easily predictable, so having a bigger number of active webhooks you may find a situation where your app is flooded with a lot of request coming in.
For example, you may have some actions in Jira that could cause a cascade effect, like deleting a project. If you have active webhooks for issues, comments and worklogs, and the project had a considerable size, you would get a lot of requests towards your app. If your app is not prepared to be scaled as needed you may face some instability.
So in short you should be able to use the 100 limit, I’d just recommend you account for the potential incoming traffic in your app.
For now Atlassian can’t really estimate webhook outbound traffic, but there are some discussions around this topic. There’s a suggestion ticket with a few ideas that could help this process going forward, so I’d also recommend you to watch and comment your use case there for added visibility.