Purchasing of a new guitar, IS NEVER A WASTE OF MONEY.
Buying of a new instrument should always be seen as a long term investment. Guitar wood will age over time giving you a nicer tone there after, when the wood pores start to breath and the density increases....
Personally, my views are that Squire Stratocaster, being a Beginner Guitarist's choice, isn't worth much upgrades, unless the one you've gotten are Limited runs or Vintage 1960s or 1950s?
Even if it is those of the Vintage Stratocaster, all the more you shouldn't mod or do anything to it.
It is not worth modifying a Beginner level Guitar. I'd rather be better off purchasing a new guitar which would satisfy a better sound need. If you like dual humbuckers and a stratocaster-ish body build. You can always look at Ibanez super-strats. You can always look at the GIO series which are more affordable if you're cash strapped.
If you're unsatisfied with stock pickups on the guitars, there's always a choice to swap them out for a different brand, different model of pickup which would satisfy your tonal needs.
Personally, I will always ADVICE AGAINST CUTTING YOUR GUITAR UP, routing or digging new holes for modifications unless you're extremely sure of what you are doing and wouldn't regret afterwards when thoughts of selling it off for money to buy new guitar.
Also, When chopping up your guitar, it is always the Guitar Tone that will be affected.
From what you have describe in your Tread. You wanted Humbuckers on your Stratocaster?
My best advice is to try out cheaper brands of Pickups like Tesla, Sky Pickups and other(I'm not to sure off yet)
You would wanna be looking at Stacked-Humbucker Single Coil Pickups( Not very sure how to package the name of this type of Pickups)
Refer to Yngwie Malmsteem for Stack Humbucker Single Coil sound.
Or Similarly, you might wanna look into the Single Coil sized Rail pickups,
http://www.teslapickups.com/?products=plasma-rs1 or
http://www.teslapickups.com/?products=plasma-rs2
I'm just advising cheaper alternative. Because, It wouldn't be worth upgrading a Squire so much.
This is just my $0.05 worth, SGD got no $0.01 so can't give $0.02...