Does mixing decks in Agricola reduce the chance of synergies?
I'm going to go with my gut response here (again) and say that mixing the decks does dilute the game, but not so much by "reducing the chance of getting strong combos"... more by increasing the chance of being dealt a powerful hand!

The key deck to examine here is the I-deck.  The other two (core set) decks are ostensibly just two piles of assorted cards, one of which contains some allegedly more difficult concepts than the other.  The Interactive Deck though is specifically designed for, well, interactivity.  If you play with just the I-deck the cards in your hand are more likely to interact with the cards in your opponents' hands than if you just mix everything together.

Let's consider the Wood, Clay and Stone Paths in the I-deck.  The Wood Path is a superb card in isolation, giving you 2 Victory Points for the low, low cost of 1 Wood.  And if you've mixed all the decks together into one mega-deck, chances are you can consider it in isolation.  The chance that someone has the Clay Path, or the difficult-to-play Stone Path, is probably small enough to discount. 

Whereas if you're playing just the I-deck, chances are high that someone else does have the Clay Path, which makes the Wood Path a much less attractive proposition.  If you use it early as part of a starting player grab, you run the serious risk that someone will take it upon themselves to out-Path you later in the game.  Which forces you to think very hard about the best time to use your Wood Path - as late in the game as possible is probably good.  Which makes the Wood Path a much more interesting card, but obviously a less powerful one...