The first question you ask yourself is what accuracy do you want. Normally you want to get into 6 to 2 deltaE range of accuracy, which does not stress the system too much.
Splitting hairs, available white balance adjustments are linear by nature, while lens spectral transmission is not. However, any dust on a lens, or any so-called protection filter you are going to use will have significant effect on the profile accuracy if the profile is calculated without those (same amount of dust, imagine that). More, most probably you won't be able to take an accurate "studio-grade" shot of a colour target, simply because of flare and white balance irregularities across the target. Expect to see either crashed blacks or loss of contrast in shadows, and non-linear white balance in shadows - if you are going to inspect the results close enough, or, better to say, too close. Different amount of flare on a shot of a target and a shot of a landscape is a given, an is also a factor that has much more influence on the quality of the results than differences in lens transmission after white balance.
Yellow glass tend to have voids in spectral transmission, and that is a whole different story. With such glass you may occasionally get odd renditions of some colours, no matter how good is the profile.
The most important factor to deal with is flare when shooting targets for profiling. Alternatively, if you have the budget, you can profile using spectral response; you will need a monochromator and a light sphere to do this. Better if you use a spectrophotometer, too. In this case you can measure the components separately, and multiply the spectral data for the sensor, lens, and any filter you will be using, calculating ad hock profiles.