The water bottles are pretty much the easiest part of my grow. Keeping my temps down with water bottles forces me to check my buckets once a day... which really helps me not be lazy and stay on top of my buckets. As they grow, your roots might form a pocket where the bottles tend to sit, but this doesn't matter.
If you don't want to fuck with the bottles either convert to ucdwc with a chiller or just switch entirely to ebb n flo or hempy buckets or something where root rot is less of an issue. If you want a more automated hands off system, individual dwc buckets are not the best.
Other than that.... no they won't fuck with your roots at all.