Something I've noticed after playing IWD for a while (I've only recently bought it, along with the HoW add-on) is that many monsters and undead that ought to have their alignment set as evil, don't (their alignment is shown as "none" in Infinity Explorer). This makes many anti-evil spells and abilities like Protection from Evil, Holy Smite, Wall of Moonlight etc rather useless in most situations. It makes sense that mindless skeletons and zombies aren't "evil", but ghouls and ghasts are supposed to be chaotic evil, and as for monsters, orcs and yuan-ti should be lawful evil and goblins, etc. chaotic evil. Strangely though the game does consider Myconids to be evil (they should be neutral)
Also, I've found the Detect Evil spell/ability to be near-useless, unlike in BG2 it only works in the immediate vicinity of the caster. This means that by the time you can detect an evil creature, it's already attacking you! The only times it seems of use is in detecting the true nature of non-hostile NPCs like the false Eldathyn in Dragon's Eye.

While you're completely correct in your assumptions, there is one error. Protection from Evil still confers its bonuses whether the creature you are fighting is evil or not. What it does not confer, (since the creature isn't evil) is the ability to prevent bodily contact by evil outsiders. So it's still a useful spell for an extra -2 to AC

Aha, I hadn't noticed that (I only ever used the Paladin ability, not the priest/mage spell, so I didn't see the description). So it's still useful, as it protects from all creatures, regardless of alignment.