I think you are mixing a lot of different concerns, not all of them related to Boost specifically:
First, should programmers (or C++ novices specifically) be encouraged to use libraries, idioms, paradigms, languages or language features they don't understand?
- No, of course not. Every programmer should understand the tools they use, especially in a language like C++. However, I don't see a lot of questions here on SO where people are encouraged to not understand the code they're using. When people say they want to do X in C++, I think it's find to say "Boost has an implementation of X which works, which is more than a homebrewed solution would do, so use that".
Of course if the question is "how does X work", the question can't be answered with "use Boost's implementation". But I really don't see the problem in recommending Boost for the former kind of questions.
I also don't see how it's even possible to use Boost without understanding what's going on under the hood. C++, with or without Boost, is not Java. Using Boost in no way protects you from the complexities of the language. You still have to worry about copy constructors, pointer arithmetics, templates and everything else that can blow up in your face.
This is nothing like what happened in Java. They designed a language that removed all the subtleties. Boost doesn't do that. Quite the contrary, it has pioneered new idioms and techniques in generic programming. Using Boost is not always simple.
About the availability of Boost, I think that's a non-issue. It is available on the platforms used in the vast majority of questions, and if they're not able to use Boost, the suggestion is still not harmful, just useless.
Further, most Boost libraries are header-only and don't require you to install the whole thing. If you only want smart pointers, simply include those headers and nothing else.
About FOSS, you have a point in some cases But I'd say this is a problem for less universal libraries that users do not have. But Boost is extremely common, and if people don't have it, they should get it, as it is applicable to pretty much any problem domain. And of course, the license is compatible with any FOSS project you care to mention.
I'd rather work on a OSS project that used Boost to do the heavy lifting than one which reinvented its own (buggy and proprietary) wheels, with steep learning curves that could have been avoided.
So yeah, in some cases, recommending Boost is unhelpful. But I don't see how it can be harmful.
In any case, I don't see how it can be even half as harmful as teaching novices to roll their own. In C++, that's a recipe for disaster. It's the sole reason why C++ still has a reputation for being error-prone and produce buggy software. Because for far too long, people wrote everything from scratch themselves, distrusting the standard library, distrusting 3rd party code, distrusting everything that wasn't legal in C.