Yes, you might get a small (VERY small) additional amount of flare with a B+W XS-Pro Clear multicoated 007m filter. There really is no other tangible impact on IQ.
But, in exchange you get:
* Weather-sealing: both the 16-35 f/4L IS and the 16-35 f/2.8L II are *not* weather sealed without a filter.
* Ease of cleaning: Got some crud on the clear filter? Spit shine it with your shirt! If you scratch it, the investment to replace is minimal. Busting out a microfiber cloth in the field isn't always practical.
* Virtual lens cap: sometimes during sessions you need to swap between two cameras quickly. Would you want to throw a camera in a bag - or have it in a holster - with no lens cap? Well, assuming you don't drop your bag on concrete, for these fast swaps there is little risk if you put a capless lens/camera in a bag if it has a filter. One shouldn't make a habit of this, but its an option you generally would not have without a filter.
* Riskier shots: 16mm on full frame may require you to get VERY close to what you want to photograph in some cases. Do you want to risk your unprotected front element in these cases? How about action shots, if you are photographing in harsh elements, or just greater confidence in general since you don't have to worry about your lens?
* In reality, it does cost a lot to fix the front element of a lens, and you will lose use of the lens while its being repaired: While some blogs have pointed out that the cost of a front element is not always that much, the labor to replace it usually is large amount and it involves your lens being out of action while getting repaired. If you are getting paid, this is not a situation you want to be in.
In my opinion, the benefits FAR outweigh the very minimal additional flare you might get with a quality filter. If you are shooting pictures of the moon at night, that is one situation I can think of where you might want to pass on a filter due to the extremely bright/dark transition (high contrast) subject matter being the focus of the picture. Every other situation, keep it on. That is, assuming you buy a good one - I only use the B+W XS-Pro Clear MRC 007m as it is color-neutral, multicoated, and very slim.