Is ignoring emails acceptable in academia?
I agree that it can be frustrating, but this  is not uncommon in a big organisation (I don't think this is specific to academia). People get a lot of e-mail, and are very busy. Answering each and every email can be a lot of work in an already fully packed day. This either leads to people forgetting, or simply ignoring their e-mail to some extent. Also remember that something might be a really high priority for you, but a relatively low priority for the person you mail. So I don't think ignoring mails is acceptable, but sometimes understandable. 

I think the best way to deal with it is to try and work with the system. If you see that professor X is very unresponsive to his mail, approach him in person. If a department does not return your mails, give them a call. This kind of personal approach makes it harder for those persons to ignore you, an email is very easy to ignore.