There seem to be few things that might require you to gain root to change with N900, but I haven't found discussion about if there's any considerations to do while considering is you're really going through this.

Personally I've been on-and-off user of linux with my laptops (mostly if I get bored and want to try something new) and I have Ubuntu server running in my study so I have some understanding about this topic, but I'm not even close to any expert.

So lets say I'm considering enabling the HID Bluetooth profile when I get my hands on my N900. Wiki has guide for it and part of it is gaining the root.

What implications there actually is once the root user is enabled in N900? Common sense tells me that I need a good password and also I shouldn't touch anything I don't know about.

But since we're now talking about a a device that has also a phone in it etc, I'm a bit more cautious and would like to know if there's anything else I should know.

If you install applications manually, you have to make sure they don't install themselves to the root partition. It's very small and will fill up with unpleasant consequences.

Root is always there, you don't enable/disable, you just temporarily gain it's super-powers.
In general, root is the only user who can utterly obliterate a linux install. The ways to do this are plentiful and impossible to completely put down on a list. Just be careful. If you're following an instruction set, follow it faithfully.
And use root as little as possible. If you think a command might be hazardous, better to ask than reflash (or better yet, google - linux is extremely well documented on the internet)
In the end, using root is like being superman - you can do very cool/useful stuff, but you can also screw up enormously. There is no guideline other than experience
EDIT: try this for homework: find out what "rm -rf /" does and why it's a very bad idea to use it. This should show you the way to look up commands when unsure

At least I have enough Linux experience for this. Like I mentioned, I still have a linux server running here without GUI. Just SSH once I get it up and running.

So basically it's not like enabling root-user in Ubuntu but more like using "sudo" or something similar.

Exactly....