Good points H.G, so I thought I would consider removing it in my engine's code to see what happens.
Opening the unforeseen consequences door, I realized that I'm using the 50 rule counter as part of the 3-fold repetition test. the 50 move counter limits how far "back" I need to test for repeating positions. without it, the 3-fold would take longer each time it is called. considering the little amount of code needed to implement the 50 rule test, in my case, it is better to leave it in.
other engine developers can make their own determination.
most engines can't "see" 50 moves ahead and will probably never have to worry about it, and I'm sure that some kind of progress will have been made long before that, if not, then the position deserves to be halted after 50 moves. 3-move rep is far more likely to come into play in most deadlocked positions.
"An Engine's strength flows from the Search. But beware, pruning, extensions, reductions; the dark side of the Search are they. Once you start down the dark path, it will dominate and consume you, as it has to so many developers before.” -- Yoda