Most SSL certificates use the same validation mechanisms as Let's Encrypt. Let's Encrypt is not less secure than other providers of domain validated (DV) certificates, all they check is that the requester of the certificate has some kind of control over the domain at the time of the request.

You couldn't trust SSL for owner identity before Let's Encrypt either, nothing has changed.

If you want stronger guarantees for the identity of the owner, you'll have to look for Extended Validation (EV) certificates (Browsers generally show the company name next to the lock in the URL bar). (https://www.cloudflare.com/ as an example, HN or https://www.amazon.com as examples of sites that don't use EV)