however when I plug in my ccr2216 with the 40g transceiver in port qsfp #1, the qsfp port #2 does not show 100G speed available only 40g.
For your setup, QSFP-1 should run in 4x10GB mode and QSFP-2 in 4x25GB mode.
I seems like running QSFP-1 with 4x10GB somehow disables 4x25GB on QSFP-2.
Most likely you discovered a bug in ROS on CCR2216.
If you see this with the latest stable (7.2.3), I suggest to contact
support@mikrotik.com.
In general, I would be carefull with running recently introduced devices like CCR2216 in production.
Out of experience, it takes some months and ROS releases for new devices to get ready for the field.