NRF24L01+ Longer wires or add antenna cable?
From my experience, there is no difference between the two setups regarding signal quality. But, I would prefer the first one, because in the second setup, you need 2.4 GHz antenna extender for about the same length of the tube, and another issue is the additional cost that it adds to the system. Whereas in the first setup you just need a few inches of normal cables which are cheaper and easier to provide.

Another thing to take into consideration is that, if NRF24L01 modules are well designed you should not care about EMI. EMI is something that you should care about with made-in-china products.

My advice is to use the first setup and test the performance of the system. If you noticed a degradation in the connection quality, take the NRF24L01 module outside the tube.