I currently have my Strat set up with Ernie Ball Hybrid Slinkys with 5 tremolo springs in the back...

Im wondering if I take out 2 of the trem springs, will anything be messed up, such as innotation, etc?

probably have to reset the action

Yes, you would need to reset the action and intonation and most likely re-adjust the spring claw to accommodate having fewer springs. Removing the two will cause the bridge to raise, pulling the guitar out of tune.

It would probably be easier to wait until you're ready to change the strings again then take it in for a set-up with the two springs removed if you're unsure of how to do a set-up. Once that is done, then changing strings on your own should be a breeze.

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Well - think about it. If you have 5 springs countering the tension of the strings and you just take out two springs, you'll have a lot less tension and the strings will pull that trem up a bit. You'll have to tighten the springs that are left to get it to that same position. After that, I'm sure you'll have to adjust the intonation (you might not "have to", but I would anyway. quick thing).