Why do organisms excrete nitrogenous wastes?
Some amino acids are essential, that is, they cannot be synthesized.  For all the others, however, you need building blocks.  Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination.  Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate).  The body has thus produced some amino acids and metabolized others for energy,  but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.

To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em.  I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full.  You could ask the same question for any substance we might eventually want.