Never implied anything else. A Zen Archer can flank someone with a bow if he's next to him. A rogue with a wand can't (even if he has a short sword in his other hand).
Zen Archer said:Reflexive Shot (Ex): At 9th level, a zen archer can make attacks of opportunity with arrows from his bow. The monk still threatens squares he could reach with unarmed strikes, and can still only make one attack of opportunity per round (unless he has Combat Reflexes). This ability replaces improved evasion.
Monk Class said:Unarmed Strike: At 1st level, a monk gains Improved Unarmed Strike as a bonus feat. A monk's attacks may be with fist, elbows, knees, and feet. This means that a monk may make unarmed strikes with his hands full. There is no such thing as an off-hand attack for a monk striking unarmed. A monk may thus apply his full Strength bonus on damage rolls for all his unarmed strikes.
PRD Combat Section said:Flanking
When making a melee attack, you get a +2 flanking bonus if your opponent is threatened by another enemy character or creature on its opposite border or opposite corner.
Please provide a rules citation for this.
Similarly, I was not able to find something to suggest that you would not threaten with your primary weapon (a sword for example) even if you were activating a wand with your other hand on that particular round. If you have a rules reference there, I would also appreciate it.
It's in the rules you quoted yourself. You only flank while making melee attacks. While you would still provide a flanking bonus to others, a ranged attack with a ray would not count as flanking and therefore be unable to get the bonuses from sneak attack unless the target were denied his dexterity bonus.
Since activating a wand of scorching ray is a standard action, the rogue might try to use his melee weapon to feint. He might even make a 5ft step after feinting to avoid the attack of opportunity for ranged attacks.
Still pathetic and expensive.
You seem to be right about the Zen Archer, however.
Jadeite said:Never implied anything else. A Zen Archer can flank someone with a bow if he's next to him. A rogue with a wand can't (even if he has a short sword in his other hand).

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.