These cheeky chappies make excellent skirmishers because of their high move rate and low cost (6pts or 7pts if you turn them into scouts)
They are needed at the very least to act as a missile shield for your core fighting units, the Temple Guard and Saurus units.
I personally never swap their blow pipes for javelins and shields. The shield does not benefit you at all against any str 4 or higher missiles and you will be trying to keep your skinks out of combat most of the time. Also you get 2 str 3 shots from your blowpipes with a range of 12", while your javelins only provide 1 str shot over a measly 8" (by the way, both are poisoned missiles) [note see excellent comment below by Warphammer]
The scouting ability for an extra 1pt is worth taking for a couple of units or more if the enemy has a lot of war machines or if you expect there to be battlefield terrain or features to hide behind or within (as close as 10 inches from the enemy !)
The thing with skinks if you need to learn how to skirmish well. Use them as missile shields and also skirmish behind units you don't want to be charged (the skinks can run around your unit with their 12" charge to prevent the enemy engaing you first)
One last thing to remember... if you do need your skinks to fight try to charge the enemy in the front and use other units to engage flanks and (if you're lucky) the enemy's rear. Skinks do not negate an enemy's rank bonus by attacking their flanks.
I usually take units of 13 which means that an enemy firing on them would have to cause 4 casualties in a phase before the unit of 13 has to test for panic. If you took 12 it would be 3. A unit of 13 gives you the same 'panic buffer' as a unit of 14, 15 or 16. A unit of 13 is also more maneuverable and you can take more units as missile shields. Even if they do panic with a cold-blooded leadership of 6 they're likely to rally before they run screeching from the battle ground.
May your skinks be blessed by the...
Mark of the Old Ones !
muhahahaha.....(in a deep wisened other worldly voice)