Sites, whether popular or not, going bust after some time is not a singular occurence on the Internet. Wasn't it Technorati that claimed that 90% of all blogs are usually abandoned by their users? Microblogging sites are not an exception. Creating a microblogging site requires more investment than say an internet forum, a wiki or any kind of website (except a full social networking site). In fact, some microblogging sites can only be hosted on their own server(s) which isn't that cheap in the long run (shared hosting is out for such sites)*. Doubt that? Then, are features such as XMPP, Jabber etc given to webmasters on shared hosting accounts? Nope. In fact, from one forum I visited some time back, a question on launching a microblog from shared hosting was raised. But the devs of that particular microblogging script could only recommend virtual private servers as the bare minimum for running their script.
Now let's turn to some African microblogging sites that have since gone under.

Twyka

Twyka.com was a Kenyan microblogging service that ran on the StatusNet software. Basically, it was targeted to people living in Africa and in the diaspora. A few months later after its launch, the service degenerated to a spamnest; it seemed to have been neglected. Terrible! Currently, you can access some of the pages on the site (the legal and documentatuion pages) but the microblogging service is not working.

Naijapulse

A Nigerian microblogging site that started out quite well but presently, one cannot access the site in any way. The site seems to have been suspended by its hosting company.

I know there are so many African microblogs out there that never got to be known and are now dead. Do you know of any?

*Starting out a microblogging site using dedicated scripts such as StatusNet requires your host to provide you with the features I have mentioned here. However, you can start your own microblog cheaply using WordPress' BuddyPress plugin. If it worked for me while using XAMMP then it can work on any shared hosting account.