The DM42 is not a physical clone of Free42, so.....

[EdS2]

It's good to see that SM are in the process of fixing up the alleged GPL violation.

On the question of whether SM could protect their own innovations: yes, they probably could. The physical design of the calculator could be protected, their name could be protected, the name of the calculator could be protected: trademarks, registered trademarks, registered designs, design patents are I think the appropriate means. It might be that something in the construction could be patented, whether a circuit or a mechanism. The PCB design would, by default, be copyright by the designer, presumably SM, if they'd put creative effort into it. The manuals would be copyright in the same way. If there were a PC-side device driver that would be copyright by its originators too.

As for the software, if they have made contributions or modifications, they have copyright there too - but if that software was licensed to them under GPL, then their modified version must also be licensed under GPL. If the software was licensed otherwise, then different rules apply.

If a calculator manufacturer wanted to make a proprietary version of an existing open source emulation for use in their product, they could approach the copyright holder and negotiate for a different license. (That's perfectly possible, and in the case of a sole author it's also practical. It might even have happened. The point is that the copyright holder has a right to issue different licenses on different terms to different people for different purposes.)