Mage shoots a Stun Bolt at a spirit when it is manifested. What happens as it doesn't have a stun condition monitor?
Mage shoots a Stun Bolt at a spirit in the astral room. What happens?

Well, to be fair, only players and prime runners have a stun damage track, but in any case, any time a spirits condition monitor is filled with damage in the material or astral plane, they are disrupted. Stun and physical damage are not really any different to them.

Unless the mage is astrally perceiving at the time, he won't be able to target the spirit. Simply being able to see it psychically manifesting doesn't allow him from the physical plane to target a mana spell on a being which is purely on the astral plane.

I think he meant materialized, in which case it's not purely on the astral and thus he can.

Wait... there are different stun rules for PCs and NPCs???

Yes. Most NPC characters only have one condition monitor, that I believe is the size of the bigger of what their stun or physical damage track would be. Both stun and physical damage go on the same track, and an NPC only dies (if I'm correct, don't have the book with me), if the final attack is physical and deals at least 1.5 time their body in damage.

It should be noted that the single damage monitor track is suggested in the rules (SR4A, p. 280) as a guideline for grunt level opposition, to make things easier for the GM. Individual NPCs of varying levels are not necessarily structured this way. Particularly for major opponents, the dual tracks are appropriate.

For spirits this is supported by the comment on page 298, under Critter Combat, where it says, "all combat rules apply equally for critters and characters." I tend to use both tracks for spirit NPCs, as they tend not to be grunt level opposition. But, then, I also tend to use both tracks for most NPCs, just because I don't want them to fall so quickly. In that regard I am not house ruling, but choosing to ignore the guidelines for making my life easier.

Spirits do have a stun monitor. Whether manifested or not:

Found that now, too that they have a stun damage track. Anyway it doesn't matter for the question after all. If a damage track is full they get disrupted: thus stun bolts rock against spirits.