The Core book seems to barely cover this in detail. I have a dual-natured Mage in my party that can astrally perceive. We have already come to some debates about whether or not he can use this to target mundane characters with spells such as mana bolt. Also we have had trouble assessing whether or not physical barriers have any effect when he does this. It seems to people at the table to be a strange loophole to be able to target anything he wants while astrally perceiving to achieve line of sight through any barriers. Any input from anyone either in a party or by a GM who has had more experience in this would be greatly appreciated.

No, he cannot use astral perception to target mundanes for spells. Mundanes do not 'exist' on the astral, therefore they cannot be targeted (just like those same mundanes can't target an astrally projecting mage).

*HOWEVER* he can use astral perception for shooting, using elemental manipulation spells, tossing grenades, etc. (at a penalty for mundane attacks). If it's pitch black, astral perception will allow him to know where the mundane is, so the mage can 'see' the target well enough to aim his uzi at said mundane.

No, I don't think so... ALL living things (magical or not) have auras, and are thus capable of beeing seen with Astral Sight and just because you are astral perceiving (you are now dula natured) it does not mean you are casting a spell into the Astral Space (you have the option to do so, but it is not mandatory)... because of this, you MAY target any spells against them in the real world (and are not even penalized for doing so due to being dual-natured)... however, any barriers that exist in the real world will block line of sight for Astral Perception, and there might indeed be modifiers to actually see your target, just like there might be in the real world (target hiding, astral/real world barriers like fog or smoke, etc.)... (See Astral Perception, SR4A Page 191; and Astral Visibility, Street Magic Page 114).

That is my read, as well.

If you were to use astral perception to try to shoot someone with a gun in a pitch-black room, are there any negative modifiers for perceiving the astral but trying to do something on the material, or does it completely eliminate the penalty for fighting blind?

You get a -2 penalty for trying to perform a mundane task while astrally perceiving.

Exactly, as Shooting a gun is not a magical action, it is penalized...

Tymeaus is fully correct. Astrally projecting would prevent him from targeting mundanes, as he wouldn't be on the same plane, but astral perception doesn't (as the mage becomes dual-natured, ie: exists on both planes at once).
And physical walls are just as impossible to look through on the astral as they are on the physical, so the situations where it actually helps with LoS are uncommon.
If you successully manage to cast a spell, though, barriers that aren't astral barriers can't stop the spell, which makes fiber optic cable nets so dangerous: If the mage can see you (naturally), he can cast spells at you, even if there happens to be a wall between the two of you.

That is only for metahumans. The way I read the OP, he is permanently dual natured, so he does not have this penalty.

Yes, rereading it, that is correct. Astral perception allows for LOS, however, barriers likely still offer concealment. This might help casting against a character in a dark room, but it won't let you target a character on the other side of even a paper-thin wall.

This is incorrect, Astral Projection allows one to perceive the real world, and any mundanes just as if you are Astrally Perceiving. This is borne out in the rules by the fact that Astrally Projecting characters can act as spotters for ritual spellcasting (p. 184-185 SR4a). When you are Astrally Projecting, however, you cannot otherwise effect mundanes, so no projecting and casting a mana bolt (or other spell) on someone on the physical plane.

If you read the quote... he said that Astrally Projecting would prevent him from targeting mundanes (mundanes are not in Astral Space)... this absolutely correct... and is exactly what you said when you corrected...

When you are acting as a spotter for ritual magic, you STILL CANNOT affect any one on the physical plane, you are just guiding the magic (so to speak) as the real effects are generated on teh Physical and take effect on the Physical...

However something to bare in mine is that there are vision mods for Astral Sight as well so you can't count on being able to sling you mojo around by merely opening your Sight Sight.

Not to mention the dangers of merely going dual natured in the first place since the majority of your team is unable to provide backup and support.

I read 'targeting' as 'viewing'. Technically, spotting for ritual spellcasting is targeting, but that is splitting hairs