With help from @aman_cc, I think I figured it out. I'll start with two buckets and then generalise from 2 to k. Sum over the number of red balls in the left bucket, $l$. For simplicity define $m=n/2$ to be the number of balls of either colour. Then the right bucket must contain $m - l$ red balls. There are $\binom{m}{l}$ ways to put $l$ red balls in the left bucket. The same needs to happen for the black balls (→ square it). There are $2^m$ ways of putting $m$ balls into two bins. Thus, for the probability $X_{2,m}$ of having an equal number of black and red balls in both bins, we obtain
$$X_{2,m}=\sum_{l=0}^{m}{\left(\binom{m}{l}2^{-m}\right)^2} = 4^{-m}\sum_{l=0}^{m}{\binom{m}{l}^2}=4^{-m}\binom{2m}{m} \leq 4^{-m}\cdot\frac{4^{m}}{\sqrt{3m+1}} < \frac{1}{\sqrt{2m}} \ .$$
We can see that the probability of this happening decreases as we add more balls (at least for two buckets), as we would expect intuitively. To prepare for the generalisation, the number of configurations with matching numbers of red and black balls in each bucket is $X_{2,m}$ without the $4^{-m}$ factor. Call this $C_{2,m} = \binom{2m}{m}$.
Then we have
$$C_{k,m} = \sum_{l=0}^{k}{\binom{m}{l}^2 C_{k-1,\,m-l}}$$
(Note that $l_k$ will always be 0 as the last bucket is fully determined, I could have ended it at $l_{k-1}$ but it looks cleaner this way). Then $X_{k,m} = C_{k,m} k^{-2m}$ is the probability we are looking for. Or rather, put in terms of $n$:
$$X_{k,n} = C_{k,\frac{n}{2}}\cdot k^{-n}$$
Thanks to @aman_cc for the help!