You are starting a fascinating journey. To begin, you will need to understand short λ/4 transmission lines, and resonant λ/2 dipole antennas.
Two equal and opposite waves of current flow. One is on the outside of the inner-conductor, the other is on the inside of the outer-conductor. That is a closed chamber. The currents flowing on the outside of the outer-conductor are external and unrelated to the internal currents.
The short-circuit end is a plane of mirror symmetry, so what is at the open end of the resonant line, (your ion trap), is seen as a negative image of the trap, λ/2 away from the real trap. You can then see the inner conductor as being a resonant λ/2 dipole antenna. You will couple energy into that transmission line, to excite a standing wave on the virtual dipole.
The coupling loop is very close to the virtual centre of the dipole, where the dipole has a voltage null, but a current node. The SMA is a virtual wormhole between the outer world, and the inner resonator. The SMA connector screen is connected to the outer conductor, inside and out, at that point. The signal from the SMA is connected inside, through a loop, to the mirror. That loop is the primary of a transformer, with the secondary being the inner conductor of the resonator. Notice how the small loop is also imaged in the mirror, so it feeds the resonator current, at the voltage null of the dipole. The SMA is 50 ohm impedance, so the loop will match the inner conductor at a 50 ohm point, close to the centre of the virtual dipole. The impedance at the open end of the dipole will be virtually infinite, so it will be all electric, no magnetic.
The ion trap will be connected between the end of the dipole, and the conductive end wall of the resonator, the end plate. The ion trap is therefore at the current null of the resonator, where the voltage node is at a maximum. Since the standing wave current is zero at the tip, there is almost no magnetic field near or in the ion trap.
You can save several weeks in the laboratory now, by studying transmission lines and standing waves, for one day in the library. Where you start will depend on your background in studying electromagnetic waves.