Our first female Bearded Dragon has given us 2 sets of eggs for the last two years. Of course she was never with a male Bearded Dragon so we knew they were infertile. We just removed them and threw them away. But if there is any chance they could be fertile then I'd remove them asap and freeze them. That way you don't have to worry about hatching babies in the odd case they had the proper temps in the landfills. That is if you are not ready to raise a bunch of babies up.
And yes it is a good idea to give them an area to lay eggs. They can get egg bound which is not good. I even had my herp vet tell me I should get my females spayed. Apparently it is possible but until my vet said something about it I never knew you could. I'd be more afraid of my BD being under the knife. But she is a vet that hates breeding of any animals.
Now that you know he is a she, you can be more prepared for future eggs being laid.
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