Can I use a CAN-bus for acquiring data.
Your bit calculations is correct, but it is important to remember overhead and bus usage. 

If you use CAN basic frames, then each message can carry up to 64 bits and has 44 bits of header overhead. This means in the most optimal case, you will need extra ~70% of bandwidth for the overhead. In reality, it may be even higher if your senders are not co-located -- for example, if encoders are separate devices on the bus, each one will only send 17 bits per frame -- for 258% protocol overhead.

Also, you should not use full bus bandwidth to leave space for imprecise clocks, error messages, etc... I have heard that you can run up to 80% bus utilization without major problems.

Overall, you are not going to get 3KHz sample rate. Consider multiple CAN busses or ethernet if you need this rate.