Disclaimer: I don't work for GrapheneOS and am not associated, etc. etc.
I don't know if there have been any announcements as to a reason for deprecating these, but I feel like the reason is rather plain - they want people using their apps instead.
The main problem I can think of with including other apps is licensing. You'd have to confirm that their licenses don't conflict with GrapheneOS' license (source), and my current favorite sms app (QKSMS) is distributed under the GPLv3, meaning it isn't legal to ship them together.
I really like the idea of "suggested apps". I don't know what the legality of suggesting apps with incompatible licenses would be, but either way, I don't suspect this will happen. Doing this might cause some people to assume that the apps are distributed/associated with GrapheneOS and that they have been locked down/reviewed for security in the same way as the OS. I don't know if the GrapheneOS team has the bandwidth/desire to deal with reviewing 10 or so other codebases, but I suspect not.
On the other hand, this would be a very nice way to help onboard users. In addition, it might be good to find a new SMS app replacement. I don't know; that's for the GrapheneOS devs to decide. But even if they decide not to implement it, remember - you can always install software yourself! Maybe I should make a "first few steps!" website which has a quick tutorial on F-droid, sets up a few QOL apps like Simple Gallery, and tells people how to install Google Services
Again, take this all with a grain of salt - I am just a random guy on the internet!