I have a bit of experience with client/server architecture and up till now all my server did was relay and occasionally verify data to it's connected clients. I have even less experience with deploying a server, I did that once on a free amazon AWS tier. Anyway, I am planning on making a larger networked game and I am wondering if such a server needs GUI, or at least a command line console and if that is even possible to run from a vpn. Another way to check and correct/alter server data is to make a separate client that logs in on the server that has all kind of other privileges and a gui of itself. I know this is a broad question but I like to know what is common so I can anticipate on this while writing my server.

Yes, you do typically need some way to query the server. What you need depends on what type of server you're talking about, where you're hosting it, what kind of people need to query it, etc. You could create a specialised client, you could have a console style login (e.g. with SSH), you might have a web interface, etc.

Thank you, could you list the pro's and cons of the different methods? My guess is a specialized client suits my needs, A web interface maybe just for the database if I ever want to create an api for it.

The pros and cons are exactly what you'd think they are. e.g. If you have a web interface, the pros are that you get to use your own browser, the cons are that you need to do everything via HTTP and HTML. If you have a console interface, the pros are that it's very simple text in, text out. The cons are that it's just text in, text out.

You need to think about what you want from the tool - again, depending entirely on what type of server you're talking about, where you're hosting it, what kind of people need to query it, and decide on the interface you need in order to meet those requirements.