As far as cars, police, Malta Transport, are concerned there are 2 types of people, tourists and residents.
At the moment you are a tourist, so can drive your car on Belgian plates for the 6 months. However, a tourist can only be here for 3 months at a time, so you need to be leaving/coming back to keep this status. You will probably find that your Belgian Insurance doesn't cover the full 6 months either, so check that carefully and contact your broker if necessary.
If you apply for an ID card, residency, then you immediately lose the tourist status. This means you can't drive the car until it has Maltese plates, VRT and road licence, because you are now classed a resident.
Although you weren't stopped coming off the ferry, there was probably a MTA official standing somewhere noting down all the foreign plates.
Keep your boat ticket in the car as proof of when you arrived. It will be useful at a roadside stop. What you don't want to do is tell the MTA that you are now living
here. That's when they will want to confiscate the car and/or give you a 30euro a day fine. They will try to catch you out by asking, "Can I see your ID card" or "How long have you been living here" or simply, "What's your home address".
As far as motoring goes, your home address is in Belgium, you merely have a holiday home in Malta.
Of course, if you are intending to keep the car, it's better to get it registered within the 3 months to save any hassle. There's plenty more info on importing/registering already on the forum.