Yes, people did start reverse engineering the companion API without permission, which is somewhat unfortunate. They also asked Frontier at the same time whether use of the CAPI was something they considered acceptable. Frontier then
said they were discussing it, and devs continued to ask over time without answer, before finally getting a reply 8 months later saying that
use of it was permitted.
I wasn't really part of the developer community at that point, but I do believe that had Frontier ever officially stated its use was disallowed, that the developers would have respected such a request.
More to the point, though... when they removed the companion app from the store, why would they have left the companion API active at all, if not to enable the community to continue to access it?
Well, the developers of both of those tools were among those whose actions (I assume) you're referring to as disgraceful. You're of course welcome to hold that opinion though; it was never exactly going to be a universally popular course of action, and rightly so.
If you look back through this thread, you'll find that all of the established tool developers who have posted in it are generally supportive of the current state of affairs. The journal is excellent, and it continues to get better. In my experience the third-party developers are very respectful of Frontier's wishes regarding what they do and don't want us to do - this is much easier now that they communicate such things more regularly.
It's fair to say that Frontier have really turned a corner in the opinion of most third-party devs (and feel free to look out for a letter soon-ish from EDCD to that effect).