The bathrooms are located next to each other because it is much easier to run the water line and install the plumbing system that way.
As for your question, the full answer is it depends.
From the perspective of the appraisal, yes it will decrease the appraised value of the home. The appraisers look only at numbers and does the house have it or not. (A 25 yr old functional air conditioner scores the exact same appraisal value as 2 month old high SEER unit). So, having one less bath will appraise lower.
However a single larger, modernized, well-appointed, aesthetically pleasing bathroom may create additional perceived value in the eye of a potential buyer.