In this case, I don't think there's any ambiguity because the intent is pretty clear.
As I'm sure you will understand, we cannot wait any longer for our order.
The intended meaning here is something like this: in the present, the email is being written by the person who placed the order. In the near future, the email will be read by the person who is supposed to be shipping the order. At that near future time, the writer is confident that the reader will understand that they cannot wait any longer for their order.
It wouldn't be interpreted to mean "you won't understand when you read the email, but at some future point after that I think you will understand" because that doesn't really make sense in the context; there's no event mentioned that would cause this change from not understanding to understanding. Here's an example where there would be:
I'm afraid I simply can't loan you any more money; you're spending it on frivolous things and you never pay me back. I know it seems harsh now, but you will understand when you're older.
Here the speaker presents a clear opinion that the listener won't understand now, but that an event (growing up) will occur in the future that will make them understand when they look back on this.
Now, as for your suggestions. Must doesn't say quite the same thing. There's a social nuance to the original phrasing; they aren't confident the reader will understand. But they say they are confident because that makes it harder for the reader to come back and say "You placed your order with us and that's final! You're going to wait however long it takes!" Since they've already approached it as "I'm sure you're compassionate toward our situation and are going to be understanding about this", they've made it harder for the company to turn around and hold them to the order. That's why they used phrasing like that, not because they actually are sure they'll understand.
So the reason must doesn't work is because it's confrontational. It doesn't say "I am confident that when you read this you will understand." It says "I am confident that you are required to understand--you have no choice but to understand." So for one thing that doesn't actually say the same thing... It isn't simply saying that the understanding will happen, it's saying that the understanding is required to happen for some reason. It's compulsory. So the two have different meanings, and the version with must is less likely to elicit the response the writer is looking for, because it's missing that subtle manipulation.
Simply omitting will doesn't quite have the same meaning, but it's close enough that it could be reasonably used in this situation. "As I'm sure you will understand" means "in the near future when you read this, I am confident you will understand." "As I'm sure you understand", without the will, means "I'm sure that you already understand, even as I write this, before you've even read it." So there's the implication that the company already knew they'd taken too long to fill the order before they were contacted; they understand already that their customer cannot wait. But this is a pretty small difference in practice; the meaning that's intended is going to be understood whether you use the will or not.
I think what's most likely to be used in this situation is can rather than will. (I get that the book was trying to give will examples, but I still feel like I should explain this.) The version with will sounds a little formal, and without it you do have that implication that they already understood. So you can take the middle road and use can:
As I'm sure you can understand, we cannot wait any longer for our order.
Here can means "As I'm sure you are able to understand, have the capability to understand, are an empathetic person who can sympathize and will understand..." You're complimenting them by assuming they're an understanding person, and assuring them that you think they are definitely able to understand the position you're in and respect it and follow through in the right way. I think this is probably more common than the version with will, and it also has another subtle difference that changes the tone of the conversation a bit.