I don't know if this is a good question or an incredibly stupid one. But I'll ask anyway.
Websites can't have more than one hierarchical taxonomy. It would be an SEO disaster. But still, some may need that feature, mainly for navigability. Not menu navigability, but site navigability (archives, advanced search, sorting, etc). I'll explain.
Say we have a tourism website that lists hotels. There are many ways we could classify them. Let me start with an obvious one: geography. But wait, which geography? Our problem starts right at the beginning. Say we decide to go straight to an administrative classification: continents->countries->regions->sub-regions->towns/cities. That's a start.
And the url works SEO-wise: mysite.com/north-america/florida/whatever-county/whatever-city/some-hotel.html
Then, if the visitor needs to know which hotels in any taxonomy term have a swimming-pool, or a webcam, or anything else, we could add a tag (flat, horizontal) taxonomy or custom fields and that's it.
Nope, that's not it.
Our administrative geographic (hierarchical) taxonomy is a logical, legitimate one. But then the user wants to know which hotels are in the Alps, but not in the whole many-countries mountain range. He/she needs to know which hotels are in the Alps->Western Alps->Ligurian Alps->some administrative region of some country. There you go, that's a "problem", because we may need to have two, three, maybe four ways to classify (hierarchically) our items, be them hotels or articles in a groceries shop. Heck, that could be a huge issue for even a tiny, very-specialized jewelry website dealing with items of four brands, four different materials, four qualities and four kinds of measures (like size, weight, calibers and uh, I don't know, number of colors!).
Now, the answer to this problem is not about having one or more Taxonomies, in my opinion. The people in charge of such website don't have a problem of classification. They have a problem of navigability and sorting. So there are two things to be considered here.
One, how you go about classifying your items. You must have a unique way of doing this. That's how indexing works, how bots are able to crawl a site, how you make your url's, etc. There's no question about having one -an only one- hierarchical taxonomy for pure functionality.
And two, how you go about navigating through your items and sorting them. This may need more than one hierarchical Taxonomy, and this (these) hierarchical Taxonomies should be there somehow and not interfere with what we could call the 'official' or 'front-end' hierarchical Taxonomy. Having a "secondary" (or even more) way of classifying items should be for internal usage only, not something that can be seen, for example, by a crawler and then have Google saying 'hey, you have three indexes and a crossed sitemap that has no sense, wrong!'.
One thought crossed my mind while writing this: is there something like "hierarchical custom fields"?
So, my question would be: on a site that must set up more than one hierarchical Taxonomy, how to deal with that and not affect SEO and other concerns?
I hope that makes sense. Thanks in advance.