I'm going to be getting a 3D scanner

[Peter Blomberg]

Of the current scan both sides are roughly the same quality, I can go better though and try to fill in the gaps as much as possible even if it will get reduced down eventually.

You sure like to overdo it. Me too sometimes. Here, it might not be necessary. The existing scan is more than sufficient for LDraw. No need to fill in those tiny gaps. I recommend you try to reduce the mesh further without doing any more scans or filling up holes. Getting down one order of magnitude to under 2k triangles would do more than well enough.