Sap removes all traces of the minion from the board since it doesn't trigger any deathrattles. Minions returned to hand lose all their buffs but there are a few exceptions. An example would be Blood-Queen Lana'thel. Her attack bonus is a permanent effect and will return as soon as she enters the board again. Silence from the owl could be better in this one niche scenario but Sap also causes a major tempo loss for your opponent since he needs to pay mana again to put the minion that was sapped in play. Blood-Queen Lana'thel is a very slow card so the tempo loss could be fatal for your opponent. Sap is not ideal for dealing with high value threats like Dragonqueen Alexstrasza though. You don't want to return minions like that to your opponent's hand.
Ironbeak Owl leaves the minion on the board and that's bad when playing against certain classes. You can silence a minion buffed by a Paladin but if you don't remove the minion (which requires a trade or another resource) they could just cast a Blessing of Authority on it. Sap in this case slows them down significantly as they have to play the minion again before buffing it.
TL,DR: Silence from Owl can be better in some niche scenarios and you don't want to use Sap on high value minions but Sap has way more upsides. It doesn't trigger deathrattles, it removes most buffs and it causes a major tempo loss for your opponent which can be fatal.