I'm really stuck on this one and haven't made any progress since Friday. If I list my reasoning so far, perhaps someone could point out the flaws in it.
First, there seems to be only one possible answer for 20a, and only one possible grid entry for 1a that ensures both entries are squares and all entries in the grid are unique.
Then, obviously we have the clue answers for 3d and 16d, and it is clear that 0 is the second digit of 19a. By multiplying all numbers of the form _3 by _8, to find the answer for 20a, there seems to be a unique solution for 17d (and clue answer for 20a), determinable without filling in any more of the puzzle.
Because 12d is the square of 1d, its last digit must be either 0 or 1, and since 16a is a multiple of 5d, I determined it must be 0. At this point I have the (apparently incorrect) permutation of all digits.
Now here's the problem; the last digit of the answer for the 9d clue answer is clearly 0 and it follows that the first digit of the answer for 7d is 0 doubly encrypted, which completes the grid entry for 6a, giving an answer which is not 12d plus a square.
I'm sorry if this is a bit vague. I didn't want to give too much away.