Yes, there's a pretty big difference. 26 inch wheels accelerate quicker, but take more effort to get going at a top speed/maintain that speed. 26 inch wheels are more agile and easier to maneuver, but 29 inch wheels roll over things better/with less effort. Those are the biggest differences for me.
For what it's worth, I prefer 29 inch wheels.
As far as tires go, if you're going to put road tires on them, you'll want a second pair for mountain biking. Road tires will be sliiiick on dirt. Tires are easy to swap in and out though. I can't comment on the bolded part because I really have no experience there, but if there's a lot of support for it on reputable forums, it's likely okay.
And giant is a really great brand! Can't go wrong with them. Just remember that if you buy used, it voids their lifetime frame warranty.
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