In almost all cases, the use of past tense in OP's example #1 has nothing whatsoever to do with the temporal difference between past and present "wanting". When you say...
"I just wanted to let you know that [statement]"
...the only semantically significant element is [statement]. Everything before that is simply deferential "distancing" of the speaker from the fact that he's making a [statement].
Since you are "letting the other person know" something, it's probably contextually obvious that you want to do this (why else would you be telling him?). And why bother to tell him you're telling him something, when that's what you're doing anyway?
The clue is in the word just. Effectively, the speaker is deferentially "apologising" for disturbing the other person, and wishes to downplay the importance of the interruption.
Using past tense is a common technique in such "formally respectful" contexts, similar to...
1: "I would have said this question is about pragmatics, not semantics"
...which is obviously less "direct" than...
2: "This question is about pragmatics, not semantics"
Note that #1 could also be expressed as "I would say [statement]", retaining the "irrealis" aspect of the utterance, but with present tense instead of past tense. Using multiple "hedges" like this is perfectly common in English, but it's important to recognise that none of it is necessary.
Probably most people take little notice of such phatic elments (particularly in written communications), so there's a risk of over-analysing here. But personally, I think I might take it amiss if a junior at work sent me an email starting with "I want to let you know [blah blah]". What do I care what he wants? He's already used up most of the attention I'm prepared to devote to reading his email, and he hasn't even told me anything meaningful yet! At least if the email started with "I just wanted to let you know...", I'd recognise it as a "standard" deferential/self-effacing introduction.
TL;DR: Phatic utterances are useful if you get them right, but sometimes you risk seeming presumptuous (if you're a junior sending unsolicited emails to equals/superiors) or patronising (if you're the boss trying to show friendliness to junior staff by addressing them in a "faux-deferential" manner). I'd avoid them.