In observing many professional theatre companies in the US, it is acceptable and occurs often for the cast to recognize the SM/crew by gesturing and applauding in the direction of the SM. In a musical, this is the last recognition, preceeded by the cast gesture and applause to the orchestra/band if it exists. As to who decides this...
I'm sure that some directors place it in the curtain call, while there are also casts that just do it because they know how much the show depends on the SM/crew.
It appears to be done less often in straight theatre. But it does happen and is not considered faux-paux. Also under the same circumstances as a musical as to who decides it's going to be done. In the last play that I worked on, the cast did not gesture towards the booth until the final performance. That night the gestured and applauded to the work of me and my assistant (the only crew). This motion was not originally placed by the director, but added by the cast.
No matter who decides to put this action in (or to not), the SM usually doesn't have a say in it. If you are asked, that is one thing, but it would be impolite for the SM to ask the cast/director for a gesture and applause in your direction. Likewise, it could be seen as rude and not in full support of the show/cast/crew/director/designers/etc... if you asked for them to NOT gesture and applaud your work. In general, as an SM an applause/public recognition is not guaranteed nor the reason we do this job. If it is offered, it should be accepted with grace and dignity for we all know how much work we put into a show. But by all means, make sure your name is in the program - that is the minimal amount of recognition we deserve and usually have no problem accepting. If you feel like the simple gesture and applause is too much, learn to deal with it - would you rather the cast pull you on stage and take an actual bow in front of a full house?
Lastly, I just saw a production of Cirge du Soliel's Corteo in which the entire cast and musicians came on stage and performed their bows. Then at the same moment all turned inwards (the show was on a circular stage and performed in the round) and applauded the crew as they ran in 2 lines (one from SL to SR and the other from Sr to SL) giving each other high fives. Not a bad way for the cast and audience to quickly recognize the crew that flawlessly (hopefully) operated an extremely technical production. (I assume that this move was definitely created by the director.)