She could be getting worked up when she's held and be breathing more rapidly, causing the noise. Clicking and wheezing of course CAN be symptoms of an RI - when coupled with mucus discharge at the mouth and nose, inappetance, etc.
Like I said, other pythons make similar noises when they are agitated as do colubrids- especially drys.
It's only when you are holding her or when you are opening her tub - correct? Like you said, it's not all the time................
The "breathing" sound can be normal. Snakes have a U-shaped wind pipe that has a slightly corrugated inside edge (as opposed to mammals that have a smooth O). This allows for the collapse or expansion of the windpipe when feeding. The corrugations are what cause the 'wheezing' sound when air rushes through with breathing. It could be due to excitement, nerves, whatever - anything thay would quicken the respiratory rate of the animal.