This was/is going to be a problem as long as the accept rate is part of visible UI. The fact that the acceptance rates is shown implies that it's a metric for grading users.
I don't like these comments much, even when they are gentle and undemanding and state the current level of the OP's rate. But you won't succeed in getting rid of them unless you have a system in place that you can point to and say "This is handled automatically".
Yes, there are the reminders on the profile page, but they don't address the pattern and don't mention the rate (do they? It's been ages since I've seen one...). SO, here are some random thoughts on what an automatic acceptance reminder might look like:
N days after an acceptance rate eligible question is asked the system checks
(!answer accepted_for_this_question) && (accept rate < R) and if the condition evaluates as true the user gets a top-of-the-screen pop-up reminder along the lines of "You have several questions with no [link to the faq]accepted answers[/link] see [link]your profile[/link]. If you aren't getting good answers [link to bount faq]consider offering a bounty[/link]."
N=4 or 5, and
R = 50%.
With a system like that in place, users can reasonable be discouraged from making such requests a regular part of their routine.
Until then, I think we're stuck with them.