Yes you can. The limit is 100 names per certificate, and each name can be any combination of regular and wildcard names. Please note that wildcard records are allowed only with DNS-based validation. This plus a limit of 50 certificates per week will allow you to cover up to 5000 subdomains per week (renewals are limited differently).
Limits in detail are described here: https://letsencrypt.org/docs/rate-limits/
So, for example with Certbot you could do (Cloudflare used as an example of DNS provider):
certbot certonly --preferred-challenges dns-01 --dns-cloudflare \
--dns-cloudflare-credentials /etc/letsencrypt/cloudflare.ini \
-d example.com,*.example.com,*.sub.example.com,*.sub1.example.com,*.sub2.example.com,*.sub3.example.com,*.sub4.example.com,*.sub5.example.com