The description for Battle Cleric's Lore says "You gain a +2 shield bonus to AC", but shield bonuses are a special type of bonus that boosts AC and Reflex. Is this an exception, or can I boost Reflex too even though it only mentions AC (in Dragon #400)?
You can't boost reflexes too, but it's not an exception.
Shields are items that add a shield bonus to AC and a shield bonus to Reflexes. This does not mean that everything that gives a shield bonus to one of the two needs to give a shield bonus to the other: it's coincidental.
Battle Cleric's Lore only gives a shield bonus to AC (arguably because it's not a shield, but that's just because we'd expect any shield to get both, not because it's universally true).