replace(X1, is.na(X2), NA)
#     [,1] [,2] [,3]
#[1,]   NA    4    7
#[2,]    2    5    8
#[3,]    3   NA    9

X1 * NA^is.na(X2)
#     [,1] [,2] [,3]
#[1,]   NA    4    7
#[2,]    2    5    8
#[3,]    3   NA    9

X1 + X2 - X2
#Error in X1 + X2 : non-numeric argument to binary operator

X1 <- matrix(1:9, 3, 3)
X2 <- matrix(c(NA, "a", "b", "c",  "a", NA, "c","f", "a"), 3, 3)

X1[is.na(X2)] <- NA

X1 + X2 - X2