Not sure if serious... It does not scan the whites of your eye (the sclera) but the iris. It looks at variation in colour and/or the radial pattern of the muscles in the iris. Thus allergies won't be an issue, but tinted contacts might (although I doubt it).
You are right with allergies, but most probably tinted lenses would not cause any trouble if they are transparent.
I have been involved in some research projects related to iris scanning and possible medical conditions changing the recognition results. The most common recognition algorithm (John Daugman's IrisCode) has proved to be very robust.
Once the image is taken, the first step is to recognize the limits of the iris (white sclera on the outside, black pupil in the inside). The remaining ring is the "unrolled" (transformation to polar coordinates) to give a rectangle. The clever thing here is that after this it does not matter if the pupils are dilated or contracted.
The colour information in the resulting image is not significant. IrisCode can be calculated from colour images, but especially very dark eyes give better contrast in NIR (slightly longer wavelength than visible light). Also, with NIR a flash can be used without blinding the person to be recognized.
IrisCode does not even need to see the complete eye. Very often eyelids make it impossible to see the complete annular area. The required resolution is also quite small, a few hundred pixels across the eye is enough. (Which leads to the conclusion that the iris patterns can potentially be stolen from many photographs. In this sense retinal recognition is safer in high-security applications.)
It seems that very few eye-related diseases change the recognition results. However, there are conditions which change the way pupils react to light, so the "alive/dead" recognition may not be very robust.
Iris recognition is probably the most practical biometric recognition along with fingerprints. One of its advantages is better compliance due to it being a non-contact measurement. In the smartphone environment it does not necessarily need any extra hardware, which is a definite plus.