Well it’s a waste of gem slots :-) I don’t see a reason why to loose AP and AG because of a 0,001 increase of spell penetration. Seems pointless to me!
The benefit of spell penetration gems on a hunter for PvP purposes is to prevent certain resists to our shots that use magic such as arcane shot, Chimera shot, and Explosive shot.
Also another example of the need for spell penetration gems is "it increases our DPS in PvP by negating enemy resistances to our spell damage attacks. For example, a player with Mark of the Wild up will resist over 14% of your incoming spell damage." (From huntsmanslodge.com) That can add up quite quickly in pvp.
SPell Penetration needed by spec:
Beastmaster : 100 Spell Pen - allows us to overcome the blessing of kings and mark of the wild, while also hitting
arcane shot at full power.
Marksman : Min 100, max 200 Spell Pen - Max will allow full power arcane and chimera shots
Survival : 200 spell pen - This will allow explosive to hit with full power.
The above info can from huntsmanslodge.com article. Similar info can be found from other sources as well.