Yes, it measures surface temps.
IMHO .... no, it does not pose a "problem". Surface water temps are simply an indicator, not THE major factor.
And, if you want/need to probe the depths for temp readings, there are devices that allow you to do so. But, I'd venture to guess that 90% of the people with units that have surface temp info provided by their units ... don't pay that much attention to them (except maybe during the spawning period, when the fish are more likely to be in very shallow water).