To "be without" is to lack something. It has the same meaning as "not have". It is usually used about things that you would want.
Peter is without his usual tennis partner, as she is sick.
(Peter wants to have his usual partner, but she isn't available.)
Present perfect has the usual meaning of "starting in the past and continuing until now".
It is not a complaint but it would be unusual to say it about something that you don't want. "Peter has been without a wart on his nose": grammatically correct but a little odd.
In the actual example "being without a mother" suggests that she died (in childbirth) and is not simply absent. That is a sad meaning, it is not a complaint, helpless or otherwise.