Can I say ≤ O(f(x)) rather than = O(f(x)) if the bound is not tight?
Technically in my paper I should say “runtime $=O(n^2)$”, but it’s somewhat misleading because people think I mean it's a tight bound


No, technically you should write "runtime $\in O(n^2)$".


  I am considering saying “runtime $≤ O(n^2)$”, even though it's technically redundant


I don't think "redundant" is the right word. In a way, it makes even less sense than "$= O(\_)$"

While you can not control your readers' misconceptions, you can try not to feed them. Why not make explicit what you mean?


  The running time is bounded by $O(n^2)$ but we suspect this bound can be improved to match the lower bound $\Omega(n \log n)$.


Or:


  We have thus shown that the running time is in $\Omega(n \log n) \cap O(n^2)$.


In formulae, my advice is to always use "$\in$" unless you can give more precise results. For instance,

$\qquad C(n) = 2n\log n - n \pm O(\log n)$

would be okay.