That sounds like it's going out of memory and is killed by the system. Especially on a low-memory device like an RPi3 this seems very likely.
For information on how to reduce bitcoind memory usage, see https://github.com/bitcoin/bitcoin/blob/master/doc/reduce-memory.md
As I don't have enough reputation to add a comment to hsmiths (correct!) answer above:
I found I had to also add a line to tell logrotate to switch users to the bitcoin user (as I run bitcoind as its own user) using the format: su - $user $group. Also as I installed the systemd service as per the bitcoin github example I had a different PID location. This ...