Fabio Massimo Ercoli Emmanuel Bernard Swarm currently supports JNDI, I haven't heard of any plans to not support JNDI. I googled a bit for "microprofile jndi deprecate" and didn't find any specific discussions but I only looked at the first 20 hits on my phone, so there could be more content out there.

I also tried a similar query for Jakarta EE and didn't find much. The only match was https://dev.eclipse.org/mhonarc/lists/jakarta.ee-community/msg00233.html, which seemed to be in favour of including JNDI but hard to know which technologies will be deprecated later.