I wouldn't be too precious about this. That is to say, if you feel like emailing the journal about clarifying the status of your publication, please do so. As long as you do it in a professional manner, space your requests appropriately over time and are reasonable about timelines, then there shouldn't be a reason for journal staff to react negatively about this. This is the situation in the Journal I help manage.
If you choose to write to the journal, I would suggest that you write first to the associate editor who's handling your manuscript. Writing to the Editor-in-Chief is tricky because you close off your final avenue of reply right away. You need to be able to escalate things, and this can't happen if you shoot an email to the Editor-in-Chief. We suggest that our authors contact the associate editor in the first instance, escalate things to the managing editor and only then write to the Editor-in-Chief.
Writing to the associate editors may provide them with the added evidence they need to poke the Editor-in-Chief into action. During staff meetings when manuscripts are discussed, it is common for us to bring to the attention of the people around the table delays such as these.
Despite @Hui's misgivings, writing to journal staff does not produce a negative effect on your present or subsequent submissions. I'm not aware of a single journal belonging to the ICMJE so petty as to have this policy (written or unwritten). Certainly, make sure you that you are professional about your contact.
Good luck to you.