So, in DotA Linken's, aka Null Stone 100% blocks PotM's Arrow, aka Valk. Is there any reason it does not block the spell in this game? The fact that it isnt directly targeted should not be an issue. It is a single target spell.
Null Stone should use a general rule of blocking things that are specifically targeted, so since Valkyrie's Javelin doesn't directly target anyone I think it should still hit. True, however, that it hits a single target.
Also Getsu is correct, the stun was the result of a dummy unit casting a Stormbolt on the enemy while a trigger handled the actual damage; therefore only the stun was blocked because the damage wasn't created with a spell.