Amsterdam - many questions!

All I can help you with here is that 2 hours is probably fine for the Dutch Resistance Museum, you could spend less if your boys get restless. I don't know of specific lunch places but you should have lots of choices on the way over.

If you can fit in a canal boat ride you and the guys might enjoy that and see a lot of the city in the process.

From what I remember of the Red Light district, the women are on display wearing skimpy clothing - not less than you see at the beach. There's fast food everywhere. A great way to see the city is to rent bikes and really feel like locals. The rentals next to the train station are more expensive. The Maritime Museum is very interesting, includes walking through a ship, and a short walk from the Resistance Museum. A canal cruise is a nice way to see the city too.

Drugs are NOT legal ! M.j. is "tolerated " in small quantities stricktly for personal use and also in 'coffee shops '. The coffee shops are visited mostly by tourists who also like to take a selfie to show their friends they were there. Locals don't go there .
Red Light district is just like any other street during daytime. Becomes ' lively' after dark.
Albert Cuyp Market is ok, just watch out for very good pick-pockets who love tourist .

Took our then 11YO Grandson to Our Lord in the Attic and must say he was oblivious to the "atmosphere" of the area. He was pretty interested in the Anne Frank House, however, it got pretty boring for him toward the end as it was swamped with people waiting for rooms to clear and very warm in the house. One thing he really enjoyed was the Museum Nemo which is just south of Centrale and a short bus ride-it's not included in the museum pass but there is an outside chess set and inside tons of hands on puzzles in both English and Dutch to match wits with, along with a "mad scientist" who built an incredably complicated domino and balloon machine that ended with everything being destroyed. He also really liked the canal tour and the Van Gohn, Rykes Museum, and the Resistance Museum. I'd suggest you get the Amsterdam pass at the tourist office outside of Cntrale for your stay.They will keep you busy!

The Anne Frank house was a highlight for me! Pick up a free booklet as you enter and read each page as you go thru the rooms. Get your tickets online before you leave. We also loved the canal tour and a Gouda & wine tasting at one of the cheese shops. Lots of amazing food- I can't remember where we ate- but we stuck with the local, Indonesian type places (I'm sure we studied TripAdvisor)