Can blessing the children friday night be done via a shaliach if a child is away from home for Shabbat?
I have no definitive source that states that this can be done. So, much of my answer is based on what I have seen as well as what I Have done and still do.
First, as DoubleAA hinted, there is no "barrier" to blessings. Anyone can bless anyone else. In some cases, blessings from a sage or rabbi are considered "holier" or "more effective", but the Friday night blessing of the children, I don't think, is in that category. If the father is there, he should do it, of course. But, there is no known prohibition for anyone to say this blessing.
I have frequently been a guest at a rabbi's home or a friend's home. The host technically considers all his guests as his own family members and all guest children at the table are as his own children. So, he blessed me as well as all the other children there, along with his own children and his wife, of course. (The wife certainly deserves a HUGE Shabbat blessing, no?)
When I have guest children in my home, I bless them as well as my own children. If you think about it, why shouldn't anyone bless the children. We are all B'nai Yisra'el - Children of Israel - after all!