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It won't make any difference to the rooster.
SO TRUE!
It would only be a problem if you have a very large rooster with a banty hen. If and when you decide to hatch chicks the resulting chicks would be mutts. Perfect for backyard flocks.
Yes it means fertilized eggs. There is no difference nutrition-wise in a fertilized vs. non-fertilized egg. You can't taste a difference and unless you know what you're looking for, you can't see the difference. Just collect your eggs promptly and refrigerate and there's really no problem...