Checks and balances are practices undertaken by governments and other organisations. "Checks and balances" can also be referred to, informally, as a practice, (in Australian English) so the meaning of the word practice is correct. Unfortunately the sentence is not gramatically correct as the verb forms do not agree. The sentence could be " What are the benefits and deficiencies of these practices" or "What are the benefits and deficiencies of this practice" or "What is the benefit and the deficiency of this practice" (assuming there is a sole benefit and a sole deficiency).

I think the sentence is just fine with the word "practices" since it's understandable and not gramatically incorrect. I should mention however that the phrase "Checks and Balances" refers to a part of the U.S. government and although it is a "practice" I believe most would think of it as form of government first. Hope this helps, sorry I don't have more to contribute.