I was watching some lectures by Joe Blitzstein (https://www.youtube.com/watch?v=FJd_1H3rZGg) that suggested working with the simplest non-trivial example. So I've worked out the answer to my question by working through a couple of examples.
Let my n=3 set be {A, B, C}. I have k=2 slots.
My permutations without replacement are AB, AC, BA, BC, CA, CB. $3 * 2 = 6$ of these. Three ways to pick the first symbol, two ways to pick the second.
Permutations with replacement are AB, AC, BA, BC, CA, CB, AA, BB, CC. $3^2 = 9$ of these. Three ways to pick the first symbol, three ways to pick the second.
My combinations without replacement are: AB, AC, BC. There are $\binom{3}{2} = 3$ of them. Three ways to pick the first symbol, two ways to pick the second, and since there are 2 slots, 2! sets of the same answers to compensate for.
My combinations with replacement are AA, BB, CC, AB, BC, CA. There are 6 of these.
Three ways to pick the first symbol. Three ways to pick the second. 9 permutations. Now, only the ones which don't repeat the same symbol are overcounted. So we only compensate for AB, BC, AC which have been counted twice. AA, BB, CC have not been overcounted by our permutation in the first place.
Thus we do not compensate for overcounts simply by dividing by k!, and our answer is NOT $n^k/k!$
So we do something along the lines of (No. combinations without replacement) + (No. of combinations with replacement excluding combinations without replacement).
But let us take the argument further.
We know the value of the first term.
For the second term, we have: three ways to pick the first symbol, one way to pick the second (the second symbol is conditioned on the first, we have effectively reduced our sample space to outcomes in which the first symbol has been picked)
So for this example, we get 3+3 = 6.
In the interest of looking at a simple non-trivial example, let us now look at four symbols G, A, T, C and 3 places to put them.
Permutations without replacement? 4 x 3 x 2 = 24.
Permutations with replacement? $4 ^ 3$ = 64
Combinations without replacement? 4 x 3 x 2 / 3! = (4!) / (1!3!) = $\binom{4}{3}$ = 4
We can list these: GAT, GCT, GAC, ATC.
Combinations with replacement: Let's start with our permutation, which doesn't overcount things like GGG or GCG. It does overcount GGC, GAT, etc.
The reason we can't do a simple divide-by-k! is that different outcomes have been overcounted differently by our permutation. It doesn't overcount strings with 3 repeated symbols the same way as strings with 2 repeated symbols and so on.
We will need to divide each of these cases by the respective overcount factor.
Where there was no replacement, we didn't have this issue, so all we had to do was divide by k!
But with replacement, you need different factors to correct for overcounting different numbers of repeated symbols.
But I do believe my reasoning leading to $n^k/k!$ is wrong. I just don't know why it is wrong, and am trying to find out.
– Learning... Apr 24 '16 at 09:22