Hi, and welcome on board. I'll try to answer your questions :
-Does using translucent layers to make, say a window or water count as "dirty tooling" ?
It depends on what you call translucent (=reduced opacity ? = blend mode a la photoshop ?) and on the person who answers.
As far as I am concerned, I consider that putting a layer with a reduced opacity to simulate water or glass is acceptable, but it wont give as good results as manual work.
-Is resizing a reference photo (or another form of visual that isn't a "pixel") and tracing a certain element [as if this were something I drew/scanned]...bad? What if you took this photo yourself? (I haven't done that, [mostly because I've pixeled like...one thing], but I draw my own stuff, just asking)
This is bad because it doesnt train you. You may be happy with the outcome but this wont make you a better artist, no matter how much you do it.
Putting the photo next to your canvas and "copying" it is a better attitude.
-What program is used for like...changing the colors of the pixel?
Most elaborate programs (Promotion, Graphicsgale, Photoshop, Pixen, Paintshop pro...) feature an intelligent paint bucket tool or a good palette manager which let you replace a color in the whole image in one click.