Heh, I could probably go a good Chinese meal right about now.
Anyways, Meta tags don't automatically mean your website can be found by a search engine. I'll try and explain this as best I can but I'm probably not the most learned person to be talking to about all of this.
Ok then, how is a software program that indexes websites supposed to find your website if no one links to it?
Unless you go to the search engine site and specifically tell the search engine to index your website then it will never find it. Even then, your only usually specify 1 URL, how does it find the other pages in your website?
Well, that's a bit of a simplification but for the most part, search engines have robots that are like web browser that randomly follow links in HTML pages and index the data they find.
Hang on, first a little bit about Meta tags...
Some search engines use the data from your META tags to list the content you say you have on your website whilst others, like google bot, index the content of the HTML page and ignore the Meta tags all together. Although the content of the Meta Tags can still end up in the description summary of the google search results, so it's good practice to use them anyways.
The problem with certain types of JavaScript menus (I'm talk about fully dynamic fly out menu systems like the one at DHTML Central that use JS to generate the <a> link elements) is that if the search engine bot can't read the JavaScript it won't be able to navigate your page as there will be no links per say for it to follow. So it'll get to the fist page of your site and hit a dead end.
As for flash, the same problem exists. The best way around this it to include a series of <a> links and comment them out, I've read that google will still follow those but don't quote me on it. Same goes for any textual content you want google to index, type it into the page with the flash and simply comment it out and effectively, google will still index that. For other search engines/bots using Meta tag should work just fine.
As for providing a non-flash version. Well, there are lots of factors to consider here. How much of your target audience has flash? How many of those without flash will be willing to download to access your content? Does your website need to be flash?
I think in your case, the latter question applies the most. Flash is all good and well, but if you?re using it because it's "easier" to provide mouse over effects then you?re using it for the wrong reasons. Flash is for multimedia content, a menu is not enough to warrant being called multimedia, now matter how spiffy you make it.
Also be warned that several search engines have penalising systems for sites that try and spam keywords and the like. If google finds the word "JavaScript" 10 times in a row, say you've put this in your keywords Mata tag, it'll drop you several ranks on the search listing for trying to spam keywords. It does the same for sites that redirect multiple domains to the same page without using a proper 303 redirect protocol and various other things people do in order to boost unwarranted traffic. Google also favours website that updates their content regularly (which is why the FAQ wikki ranks so well) and a whole handful of other things.
Search engine ranking, indexing and placement are chapters of web design all to themselves really.