Adam, you are right to be confused. The mainstream backpacking market sells some very heavy, expensive and unnecessary things. Double walled dome tents for summer, 1 pound backpacking filters for crystal clear alpine water, goretex jackets for ocassional rain, and such.
"I've always been concerned that running shoes, sandals and other less supportive soled shoes would lend to bruised feet and or sore arches."
It's all about conditioning. I am at the extreme end of this. I hike in extremely thin and flexible shoes (3mm sole) and it's like walking in traditional moccasins. It took a while to condition my feet for that.
Your arches are meant to support themselves and arch support is just a crutch for them that can cause them to be weak.
Now by all means, you should use what you are comfortable with. Shoes are a very personal thing. I hike with a gear who hikes waterproof steel toed boots, a guy who wears running shoes, and a guy who wears vans sneakers. It's preference. I'm not against boots at all, I just think it's ridiculous that so many people consider them a requirement for hiking.
Don't ruin a trip by wearing shoes that your feet aren't conditioned to use.
Waterproofness:
Once you get over the idea of wet feet and just accept it, you will feel liberated. I have done multi-day trips where my feet were wet constantly and it was never a problem for me. Wet feet doesn't mean cold feet. Your feet produce a ton of heat and wool/synthetic socks do insulate your feet well while wet.
If you are hiking in frozen or snow conditions it's different, but even then some gore-tex socks will keep your feet warm.
Also if you are hiking in warm weather, non waterproof shoes will be much cooler and less sweaty. If they get wet from rain they will dry very quickly when the sun comes out.