Yes - that makes sense, and helps people find and distinguish related questions.
I think the answer to this question will change over time. In my view, it would be useful to tag questions relating to unproven alternative currencies with the tag "alternatives", but a longer lasting currency with a larger team of developers (like namecoin) should really be tagged with its own tag as well and in the long run won't need to be tagged as "alternative". Of course, then the name of the site might be best changed...
I'm torn. I hate the idea that every question tagged Namecoin will have to also be tagged alternative-blockchains. But I hate the idea that people who search for the alternative-blockchains tag won't find questions about Namecoin.
My slight preference is that alternative-blockchains be reserved for questions about alternative blockchains in general. Questions about a specific alternative-blockchain should be tagged with the name of that chain, if such a tag exists.
I think the "alternatives" tag is pointless and harmful, and it would be better to have specific tags for each currency.
This is because it encompasses both currencies with a sane goal that make sense, like Namecoin, and stupid currencies with no other reason than to "play" like tenebrix and the like.
I don't think it's fair to put them in the same bag.