Based on the answer to this question about covering ones eyes for the Shma said early in davening, it would appear that one only covers his eyes when saying the verse of Shma in order to enhance the kavannah in order to fulfill the obligation of saying Shma. If he will be able to say the Shma and its blessings within the proper time, he need not cover his eyes when he says the verse earlier in Davening.
One of the reasons we insert Shma in the kedusha of musaf (according to the research I did for this question) is because its being said had been outlawed. If so, then saying it in musaf became the time to fulfill the obligation of saying Shma -- would the eyes have been covered then?
And in Kriat Shma al Hamittah (according to the handy Artscroll siddur) one must cover his eyes as well -- and yet this recitation is NOT about fulfilling that obligation to recite the Shma, assuming ma'ariv has been said at a late enough time. So why would there be any eye covering there? If it is simply about kavannah when davening, wouldn't it be appropriate to cover eyes ANY time we say the verse?