Kajihara obtained in 2004 a remarkable transformation formula connecting multiple basic hypergeometric series associated with A-type root systems of different ranks. By specialisations of his formula, we deduce kernel identities for deformed Macdonald-Ruijsenaars (MR) and Noumi-Sano (NS) operators. The deformed MR operators were introduced by Sergeev and Veselov in the first order case and by Feigin and Silantyev in the higher order cases. As applications of our kernel identities, we prove that all of these operators pairwise commute and are simultaneously diagonalised by the super-Macdonald polynomials. We also provide an explicit description of the algebra generated by the deformed MR and/or NS operators by a Harish-Chandra type isomorphism and show that the deformed MR (NS) operators can be viewed as restrictions of inverse limits of ordinary MR (NS) operators.