Well no, in fact if the evidence doesn't warrant charges they may never lay charges at all. However, normally if you have clear evidence of a crime in hand then it is normal practice to lay charges. If they raid the den of a drug dealer and find an illegal meth lab, charges are usually laid immediately, not several months later.I think your assumption is that the minute they have any evidence they are required to lay charges immediately.
In this case my understanding (which may be wrong) is that it's a crime to have classified documents in your possession in the manner he did and that they recovered such documents during the raid. That seems fairly clear cut.
Also they want to go through the whole bunch too to make sure they lay the right charges. If they lay a serious charge they lose the ability to lay a lesser change (I think) unless they do it at the same time.
I'm fairly confident that's not quite accurate. I'm pretty sure they can amend charges at any time I do get the gist of what you're saying, it's like if someone kills someone else is it murder 1 or 2 or 3 or manslaughter etc, and sometimes that takes a little thought. Although in such cases they usually just apply all of them and let a jury sort it.
There may well be some process that needs to happen or something that isn't immediately clear given that these are confidential records so you can't just show them to a grand jury and say 'look at what he had', so maybe there's some sort of hold up in that regard i don't know about but normally when you have evidence of a major crime in hand you charge for that crime. And the sooner the better in this case, the speculation is ratcheting up the heat again in the states and that always seems to have nasty consequences.