Is it rude to ask the associate editor about manuscript status for second time?
I think it should be fine to inquire (politely, of course) at this point. While it may be a minor irritant, it should not affect the outcome of the acceptance decision provided the journal follows ethical practice. 

If you have a decision to make about the paper it is important to get the information. If it is just to ease your uncertainty then you could also let it go a bit longer. But there shouldn't really be a downside. Maybe a note would get the editor to prod the reviewers a bit.