thank you for the information.
I found an old topic (concerning EB2) http://forum.erlerobotics.com/t/solved-stream-rate-for-imu-data/724
It shows the mavsys command, that allows to choose the framerate (streamrate), but it is not recognized with my EB3.
Anyway the link may be interesting.
I encountered a solution by calling /mavros/set_strem_rate service (part of mavros sys_status):
rosservice call /mavros/set_stream_rate 0 50 1
It seems that maximum FPS allowed by APM is 50Hz. I checked and yes, a higher value gives the same streamrate in rqt.
First, I will try to work at 50Hz, then if needed I will look for a way to get more.