That all depends on what you want yourself. DA did this on new installations so SSL would work to begin with. So especially for beginners imho.
The local nameservers are just created to DA can use something to work with so the hostname nameservers are choosen.
Normally if you get a bit more experienced, you can create your hostname before DA installation.
However, the da.direct domain does not belong to you it's from DA. You can work with it, but if you want to run your own ssl and also with e-mail you might run into issues.
So if you ask me, I would suggest to start beginning creating your own HOSTNAME, which also should change those namservers to your own. However, I wouldn't use ns1.server.yourdomain.com but just ns1.domain.com and so on. Just to keep things a bit easier. This is not required, you can also use ns1.server.yourdomain.com if you like that better.
So if you change the hostname, I would most certainly change the nameservers too. And I would strongly advise to use your own hostname.
I've helped you with that before, so you should be able to do that now.
As for the USE of nameservers for your domains, that's another question. You can create and use your own nameservers which makes life a lot easier for you, but you can also use external nameservers. That's your free choice.
