By RAW they cannot. Magical Lineage specifies that it can only be used with metamagic feats.
I also recommend against house ruling this to be allowed. It is important to recognize magical lineage and spell perfection become very broad when they are applied to effect words. Normally these abilities only apply to a single spell, but if they apply to effect words they can potentially apply to a wide array of spell combinations, as several effect words can be used to make up a single spell.
Consider that PC 1 know's word A, B, C, and D and PC 2 (who doesn't use words of power) knows spells 1, 2, 3, and 4. Say that PC1 has magical lineage on word A and PC2 has magical lineage on spell 3.
PC 1 gets the effects on magical lineage on any spell that uses word A (ab, ac, ad, and abc), while PC 2 only gets this benefit when casting spell 3. In this case this makes magical lineage and ESPECIALLY Spell perfection FAR FAR FAR more powerful than they would be otherwise (Especially considering an effect word like one that would be used to specify how the word combination targets enemies would be used in almost every combination).
I think a more reasonable house rule would be to allow these to apply only to a unique combination of words, which can't have any extra words attached (say allowing ABC to benefit, but not AB or ABCD).
Effect words are only part of a World Spell, so I'd rule that they can't be picked for things like Spell Perfection.