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Dowel + Minifix or Rafix are very strong. It's they type of joint you see on a lot of commercial furniture. There are lots of machine options to add these fixings to panels but that's a different type of woodworking.
If you use dowels and glue joints it's usually very strong too. But you need to clamp up large panels for the glue to be effective. I prefer the 'knock down' approach as it makes the furniture easier to move which means it's still useful even if the clients needs change.
I use the domino system from Festool with Rafix from Hafele to hold it together. Doesn't work quite as well with ply but still works. I only make one off custom though so no prototyping.
You could have the cnc cut small blind mortice and use loose tenons which is basically what the domino system is. Or go Ikea style and use dowels.
As far as supporting weight is concerned you'll need to look at your spans but guessing that is under 1.8m wide you should be ok with 18mm weight bearing surfaces.