Hovering over buildings isn't necessary, you will eventually learn to make rough estimations in your head. The numbers you see when you do hover over do not include power/shipping costs (as far as I can remember) as those are listed separately.

It's really not necessary to do any math in this game imo, contrary to what one might think when they learn that it's a game about numbers. Your example I guess is quite good in that sense. Say glass is worth 120$, silicon is worth 100$ - it's obvious that glass cannot be profitable. if silicon was 60-80$, then due to adjacency bonuses you could make some profit. If silicon was 20$, then glass surely would be quite profitable (unless oxygen is skyhigh). When it comes to stockpile - you need to make an assumption on just how much you have. If you can completely crash the price if you sell all of it down then you can safely keep your glass kilns working, If you only have a 100 units and the price is 100$ then yes, perhaps it's best to slow down with glass and get some more silicon in before others capitalize on this high price (even if you are overproducing silicon slightly). Stockpiles are a tricky thing, it's usually good to keep one, though sometimes you do end up with just too much stuff (like that 1000+ of aluminium that so, SO many players end up with by the end of the game, while alu never gets out of hand in the first place). Those are some good questions, wish I could give you a better answer on the exact math behind those things, but again, eventually you just get used to it and have no necessity in exact numbers.

Price at the building list is a pointer what to go for when you don't have the building yet. Relevant is the factory on the map.
Afaik both power and fuel (if any) are factored into prices, you see net revenue with fully loaded freigthers.

Having a cluster of factories increases output, but not resource consumption (except fuel). This means if you have 3 factories with 75% bonus, you get 2.25 * output for free. Now price levels suddenly matter a lot for cash flow - whether glass is at 160 or at 350, even if the "profit" displayed in the building list is 0.

The big question is opportunity cost - is there a better, more profitable use for the claim? Reorganisation is not free - you lose building materials and production time, so the difference should pay for this fast.  (When resource prices colapse, it may be an option to substitute production with energy it its in nirwana. Most resource buildings were free anyway). Is there a solid good you can produce at a profit? How much will building it cost you?
If there is an obvious answer - maybe food - go for it.

First question: why are silicon prices so high? Are there too few resource claims on the map, or was there a solar power spending binge?
Next - why is glass so unprofitable? Is there overproduction from your competition? Are HQ expansions imminent, driving up prices soon, or important endgame buildings coming up? Do most of HQs not use glass? How expensive is oxygen? If there is still good demand but competition, one answer might be to take out their production via BM sabotage. Or kill their silicon supply. Or manipulate prices that they switch production...

In the long run raw material prices usually drop low unless there is a systematic shortage; when the building is done there's almost no consumption except for manufactured goods. On the other hand colony consumes manufactured goods, so prices usually don't collapse completely.