The manual talks about Planet Classes like Desert, Terra, IceWorld, Oceania etc but now planets are described differently (subterras, lacustrine, etc), so are the Classes still relevant to the current version of SE?

If I remember correctly, they technically still work but will be converted into the new planet classification system. 

Detailed information can be found here: http://spaceengine.org/news/blog170924/
But essentially, the new classes are Terra, Ferria, Aquaria, Carbonia, Jupiter, and Neptune. The link I posted gives a good explanation as to why the system was changed and what the new classes represent. 

If you want to be as accurate as possible, I suggest using the new class system. Hope this helps!

I was wondering the same thing. The manual seems outdated.