Management has very valid concerns. It sounds like you definitely do have problems.
Taking up to an hour to reconcile deletes and/or unread marks from desktop to handheld is certainly not normal. It's an indication that something is wrong.
Before you tell management "that's just the way it has to be" you should certainly consider whether you want to keep your job or not. A line like that is going to ruffle some feathers for sure, especially since it's an incorrect statement.
What kind of load is your BES under? How is your environment set up?
You indicate Domino 6.5.6 and BES 4.1.4, but only specify one piece of hardware in your post. Are you running BES on your Domino mail server? (That would be ill-advised.)
Where's the BES database? Are you using MSDE or MS SQL? Is that also on your Domino Mail server?
Please describe your environment in a lot of detail, and we'll be able to offer some more sound advice.