Minimum value of $r$
For each $s\in \mathcal S$, let $w(s)$ denote the number of subsets in the list $S_1,\dots,S_K$ which contain $s$. Note that $r$ can be computed as the number of ordered triples $(i,j,s)$ such that $1\le i<j\le K,1\le s\le N$, and such that $s\in S_i\cap S_j$. Counting $r$ in a different way, by summing over $s\in \{1,\dots,N\}$ the number of pairs $\{i,j\}$ such that $s\in S_i\cap S_j$, we get
$$
r=\sum_{s=1}^N \binom{w(s)}2.
$$
We want to minimize this sum, over all choices of subset lists $S_1,\dots,S_k$ for which $|S_i|=n_i$ ($1\le i\le K$) and $\bigcap_{i=1}^K S_i \neq \varnothing$. The intersection condition means there exists $s\in \{1,\dots,N\}$ for which $w(s)=K$. Without loss of generality, assume that $w(N)=K$, so
$$
r=\binom{K}2+\sum_{s=1}^{N-1}\binom{w(s)}{2}.\tag1
$$
The sum numbers of $w(1),\dots,w(N)$ must be the same as $\sum_{i=1}^K n_i$, by a double-counting argument. This means
$$
w(1)+\dots+w(N-1)=\sum_{i=1}^K(n_i-1).\tag2
$$
Using the fact that the function $x\mapsto \binom{x}2$ is convex, you can show that $(1)$, when subjected to constraint $(2)$, is minimized when the numbers $w(1),\dots,w(N-1)$ are as close to equal to each other as possible. Let $T=\sum_{i=1}^{K}(n_i-1)$. For the optimal distribution which minimizes $(1)$, each the value of each $w(s)$ will be either $\lfloor T/(N-1)\rfloor$ or $\lfloor T/(N-1)\rfloor+1$. The number of $s$ such that $w(s)=\lfloor T/(N-1)\rfloor+1$ will be $T\,\%\,(N-1)$, the remainder upon integer division of $T$ by $(N-1)$. This all proves that the minimum value of $r$ is
$$
\boxed{\binom K2
+(N-1)\cdot \binom{\lfloor T/(N-1)\rfloor}{2}
+(T\,\%\,(N-1))\cdot \lfloor T/(N-1)\rfloor.}
$$
To be complete, I should say exactly how we choose the subsets $S_1,\dots,S_K$ such that the even distribution of the numbers $w(1),\dots,w(N-1)$ is obtained. Place the numbers $1,\dots,N-1$ in a circle. Starting with $1$, walk around the circle, placing the first $n_1-1$ numbers you visit in $S_1$. After placing the last number in $S_1,$ continue walking, placing the next $n_2-1$ numbers you visit in $S_2$. Continue in this fashion until all of $S_1,\dots,S_K$ are chosen. Finally, remember to add the number $N$ to all of the sets $S_1,\dots,S_K$.
Expected value of $r$
Using this answer, plus linearity of expectation, we get that when the sets $S_1,\dots,S_K$ are chosen independently such that $S_i$ is equally likely to be any subset with size $n_i$, then
$$
\mathbb E[r]=\frac1n\sum_{1\le i<j\le K}n_in_j.
$$