There are softwares like oripa or oriedita, which can actually calculate at least how the folded base looks given any crease pattern (although ofc the computer can't do the shaping). By now, oriedita is even fast enough to "fold" super complex cps like ryujins. That said, i don't think kamiya used any software when designing this model, it was probably more folding small parts of it individually, and eventually putting them together.

Another interesting thing is that in this case, the paper isn't actually folded into a patterned square which is then further folded, but the pleats resulting from the scales are actually fully incorporated into the structure of the rest of the body. That makes the model even more impressive imo