d=Dataset[<|"r1" -> <|"c1" -> 8, "c2" -> 7, "c3" -> 9|>,
   "r2" -> <|"c1" -> 4, "c2" -> 10, "c3" -> 5|>,
   "r3" -> <|"c1" -> 2, "c2" -> 9, "c3" -> 6|>,
   "r4" -> <|"c1" -> 9, "c2" -> 1, "c3" -> 1|>,
   "r5" -> <|"c1" -> 9, "c2" -> 4, "c3" -> 4|>,
   "r6" -> <|"c1" -> 9, "c2" -> 7, "c3" -> 2|>,
   "r7" -> <|"c1" -> 2, "c2" -> 4, "c3" -> 2|>,
   "r8" -> <|"c1" -> 9, "c2" -> 6, "c3" -> 4|>,
   "r9" -> <|"c1" -> 2, "c2" -> 1, "c3" -> 6|>,
  "r10" -> <|"c1" -> 9, "c2" -> 1, "c3" -> 2|>|>]

Transpose /* Query[All, Counts] /* Transpose /* SortBy[Keys]@d

<|1 -> <|"c1" -> Missing["KeyAbsent", 1], "c2" -> 3, "c3" -> 1|>,
  2 -> <|"c1" -> 3, "c2" -> Missing["KeyAbsent", 2], "c3" -> 3|>,
  4 -> <|"c1" -> 1, "c2" -> 2, "c3" -> 2|>,
  5 -> <|"c1" -> Missing["KeyAbsent", 5],
         "c2" -> Missing["KeyAbsent", 5], "c3" -> 1|>,
  6 -> <|"c1" -> Missing["KeyAbsent", 6], "c2" -> 1, "c3" -> 2|>,
  7 -> <|"c1" -> Missing["KeyAbsent", 7], "c2" -> 2,
          "c3" -> Missing["KeyAbsent", 7]|>,
  8 -> <|"c1" -> 1, "c2" -> Missing["KeyAbsent", 8],
         "c3" -> Missing["KeyAbsent", 8]|>,
  9 -> <|"c1" -> 5, "c2" -> 1, "c3" -> 1|>,
 10 -> <|"c1" -> Missing["KeyAbsent", 10], "c2" -> 1,
          "c3" -> Missing["KeyAbsent", 10]|>|>