Yes, Abrupt Decay and Loxodon Smiter spells can be targeted by spells and abilities that would attempt to counter them.
When the spell or ability that would counter AD or LS resolves, the instructions of its effect are performed as normal except for the instruction that would counter AD or LS. That one is skipped.
609.3. If an effect attempts to do something impossible, it does only as much as possible.
Protection prevents
- Damage
- Enchantment/Equipment/Fortififcation
- Blocking
- Targeting
"Can't be countered" prevents
- Countering
As you can see, there's no relation whatsoever. Something with protection can still be countered. Something with "can't be countered" can still be targeted.
Simply states those abilities function on the stack
Abilities of permanent cards normally only work when the object is on the battlefield [CR 112.6]. But you can't counter something on the battlefield. This rules makes it so theLS's ability works when it needs to work.
it makes no mention of giving the spell with the ability protection from spells.
And nothing else does. It does not have Protection.