1) Is it OK if i make short URL for almost every article in my Joomla! site like http://myjoomlasite.com/4rhd789d?
2) Is it OK if some of the articles has more than one menu?
3) What is the best way to make short URL in my site?
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1) I believe it's not OK, but acceptable and it's up to you to decide. I mean SEF URLs are good for SEO. And SEF mostly if not only stands for human readable URLs. And short URL's are not. So they are not SEF. So they are not a best practice for SEO.
2) No, it's not OK as long as there are not 1 "menu item" and all other are "menu item aliases". It can cause trouble: main would be content duplicates on different URLs.
3) Create menu item for each article with "short" alias. Or create "main" category which will contain all articles, and set this category for "home page". As result - article URL would be site.com/article-alias. And you just need to set "short" aliases for all articles.
1) There is not a short answer on this, and actually not sure what exactly you have in mind. It is to have all URLs like this, or to have short URLs as complementary to the default urls.
Usually a URL is more effective SEO-wise when it contains keywords and is meaningful and memorizable somehow.
2) It's not ok - actually it doesn't make real sense and it's not going to work well. It is the alias menu item type designed for this purpose - so you can have more menu items in the same or other menus, linking to the same content.
3) You can manually create short alias for your articles, menu-items, categories. This way the main (default) url for your pages will be shortened. If you want to have complementary short URLs that redirect to the default URL, then you can use something like sh404SEF which is able to generate automatically short-urls.