You'll have to update eventually, for security or whatever, so you might as well do it every day/week. Problems are easier to spot and roll-back with small incremental updates, compared to traumatic system reloads.
Maybe you have an easier way to keep up with your configuration files? I just use etc-update after emerge. I find that the biggest drawback to emerges is when there have been significant configuration file changes - sometimes you have to relearn their whole config file.... ugh
-Steve
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