Most woodworking books will adopt a ground-up approach, teaching a range of traditional joinery techniques to begin with, may illustrate examples of where such joints are used in everyday projects and/or give projects that use some or all of them.
Joints are generally presented from simplest to most complex, so for example a modern book that's a little simpler will usually have butt joints first, then maybe overlap joints (half-laps), housed joints (rabbets and dados), then mortise-and-tenon joints, with dovetails often left to last. In addition to going up in strength these joints increase in difficulty and complexity so they make a good training progression.
If you search for "best joints to use", often the results have a lot of joints that would require specialized tools one might not have access to.
Few joints actually require specialist tools, although it depends on what you define as specialist. As should not be too surprising all traditional joints in both Western and Eastern woodworking can be accomplished using just a core set of hand tools — basic layout tools (rule, gauge, pencil, marking knife etc.), one or two saws, a couple of chisels and a hammer or mallet. That's literally it in terms of what's absolutely required, and all the joints listed above (and many more) can be done using only these if necessary.
Obviously for producing some joints additional tools are very helpful, e.g. a rebate plane for rebating/rabbeting work, a router for housing joints/dadoes. These additional tools may be thought of as specialist when starting out but they are considered fundamental tools for a fully equipped workshop and would be on a "next tools to get" list after the basics are covered.
Given a certain set of tools and known structural demands, how does one identify the best joint to use for a project? Is there some kind of flowchart or table?
There may be such a thing but I don't think you need to hunt for one.
A good starting point here is the realisation that much joinery is an exercise in over-engineering, which is to say that furniture joints are regularly far stronger than truly needed given that most furniture just sits static almost all of the time. And when it comes to withstanding movement joints are still often stronger than absolutely required. So based on this you can often choose the least strong option and still end up with a perfectly reasonable result, depending on the requirements obviously.
Now you can come at this from a completely different direction — if you always pick the strongest suitable joint you'll never need to worry about strength :-)
Most amateur woodworkers building for themselves aren't particularly worried about making stuff that will last and last, and TBH I think this is appropriate. If one or more joints in a project were to fail say 10 years down the line that's not necessarily the end of the world since you might be ready to get rid of the thing at that point anyway. That's not to say some simpler joints can only last that long but until you start to make stuff with the deliberate intention of it enduring ("heirloom pieces") you probably don't need to worry about what is the best joint for a given location*.
Some joinery is not just about strength
Some joints are intended to be seen, and have been and continue to be a means for the workman to show off their skill. The most obvious example I'm sure is through dovetails, which even if simple in form can still show great skill if done with precision resulting in a super-clean result.
*Once you do get to this point you should be knowledgeable enough (through education and experience) to be able to unthinkingly pick a suitable joint, or you'll be building from a plan where each joint is specified and you just stick to the plan.