Hypixel.net is both their website and mc server adress.
Is it just that https is on port 443 and minecraft is on port 25565?
And if that is the case, can i do something similar by making a reverse proxy have two seperate server blocks for the one domain, with different ports?
Why not? They are 2 completely separated set of ports. You can have a service listening on port 88 TCP while having another listening on port 88 UDP and they never know about each other.