Is this effective organisation for my website?

You do realise that it will take a lot of work ot teach people a language through articles?

But it is a pretty good idea though.

The www.yourdomain.com/languagename seems like it looks better, plus people will/should be able to find all the languages sections on your blog homepage anyway.

Personally I'd go with option 3, which is: www.languagename.yourdomain.com

Since you're going to want to get each site listed in its local search engine (Like google.de for example) it's going to be easier to have multiple regional sites, rather than one site covering all regions. Option 3 is exactly the same from a design and administrative perspective as your option 2, using WPMU set for sub-domains instead of sub-directories.

Categories in WP are exactly for what you are asking...

example.com/languages/spanish/
example.com/languages/tagalog/
example.com/languages/sanskrit/

example.com = domain
languages = category base (see details on your Permalinks page in wp-admin > Settings)
sanskrit = category name/slug

Which means your posts (articles) would be like:
example.com/languages/sanskrit/first-article-here

Another way to do it is using Pages and sub-Pages in parent/child hierarchy... but be aware Pages don't send ping about new and updated content, don't have feeds etc.

You are mixing unrelated things, sorry.

No, the database doesn't care if it's shared by different categories. And a proper hosting package can handle several thousands posts...

Your plan is nonsense (10x4=40 articles per day): that's not the organic growth of a website... that's content spam. But it's your site, you decide.

Finally, what is in the database and what will be displayed on your homepage - are totally unrelated. Display = theme/design/layout.

If you go down the route suggested by Istvan above you'll hit a couple hurdles. It's certainly doable and the simplest option but I'd give it some thought before you jump in.
For example, if you're using HTML/Text widgets, then you're going to need to use a plugin to control which pages they appear on. So you don't want your German widget to appear on your Spanish language page. There's a plugin called 'widget logic' to help you with that.
Next, you may want to have a specific language somewhere on the actual theme/template. So you'd need to create a theme for each language then use a theme switcher plugin for all the pages. That's a pain in the rear. You assign a theme to a specific page but I don't think you can assign one to a specific category.
Then of course there are little details like footer texts, and any other language specific texts which you'd want to keep organized somehow.

But my issue would be with search engines and how they'd handle your multilingual site. I think breaking the content up over sub-domains will give you a better platform in terms of organization and SE visibility. But that's certainly a little more complex, and as Istvan rightly says, WP has categories to help you manage your content.

Well, with what rooze is saying we are getting into the "assuming" territory...

Just because it is a language-learning site... it doesn't necessarily mean it requires theme(s) displayed in multiple languages. Trust me, as a former language teacher I know what I am talking about

The content of different articles may or may not be entirely in a foreign language (depending on the language acquisition method suggested by the site) but the overall navigation should be in the language of the main target group: English?
Hint: if the site is publishing articles for beginner students of Japanese and the menu suddenly switches into Japanese on the Japanese lesson Pages/posts/category - that would drive crazy every would-be student

That quote from the OP doesn't really tells me there would be lessons in different languages. There will only be lessons/articles ABOUT how to learn languages... and a later post suggests the OP will be writing the articles (presumably, in English) - so no need for over-complicating it with multilingual issues.

All articles/theme will be in English. There may be the odd article in another language, however nothing too major.

I think this is a great idea, but might work better as a companion for people who are already in the process of learning whatever language they are interested. Like Ryan said, it will be very difficult to teach (and learn) a language through articles alone.

Perhaps offering videos would work in addition to the articles as well? I don't know enough about teaching language to go into detail about these suggestions, this is just my opinion as a consumer and as a person who loves language.