After update to OS X Server 5.0.3 ports 80 and 443 closed
I haven't seen similar and I have server 5.0.3 running on both 10.11 and 10.10 and those ports are open with no changes needed by me.

I would start with checking your Access for defaults on the server level and perhaps making a change to see if it propagates.



Then check the particular service that is running. port 80/443 can be opened for Profile Manager, Xcode, Wiki or Web Server so you might want to check them all before going to the logs to look and see if there is an error message.