Well, as I recall Saruman wasn't their first experience of the world outside the Shire. Their has been the Fell Winter when the wolves crossed the river Isen and had to be fought be the Hobbits. THe Hobbits had also fought a battle against the orcs of mount Gundabad (when the Bullroarer invented the game of golf by hitting an orc's so hard it flew a hundred yards into the air and vanished in a rabbithole). And last, the passing of the Ringwraiths through the Shire would be an experience to remember as well, especially since buckland raised the alarm for the first time in ages. So, I don't think the Hobbits actually lost their innocence in this matter.
What did happen I don't know. It could have been a hundred things. I mean, look at the Ents. The have been around for ages and now they lost the Entwives and are dying out.
However, even Tolkien doesn't know wether their are Hobbits nowadays. When he gives an explanation about them in the Hobbit he says:
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I suppose Hobbits need a description nowadays, since they have become rare and shy of the Big People as they call us. They are (or were) a litte people...
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greetings,
lathspell