Question: Let's say I have standard scenario of commerce site that has categories on the left and items on the right.

What I would like to do is that when user clicks on category it will pass it's ID to js, js will get all items from API by using that id and load them very prettily to my content.

It looks all cool and pro but what is the situation from SEO point of view?

AFAIK google bot enters my site, sees I have span with categories and that's all?

Answer: 
What URL can users bookmark to get back to that *item* and tell their friends? What URL can search engines index to show that item in the SERPs?

I would have said that an e-commerce site should be implemented initially so that it *works* without any JavaScript at all. You click a category (an HTML anchor) that makes another request and the server returns a page with the items in that category. Your site is SEO'd and works for everyone. Your site *is* "pro".

You then want to make it more whizzy and implement AJAX as a *progressive enhancement*. If JavaScript is available and AJAX ready then assign behaviours that override the default action of the anchors that submit requests to the server. The requests are now submitted by JavaScript, but the underlying search engine friendly HTML is still the same. Your site *looks* "pro".

When developing the site in the beginning keep in mind that you'll want to implement AJAX on top later.
You can use lynx or the tool in google webmaster tools to show you what google is seeing.
(The content you load via AJAX will not be seen by crawlers).

PS, you should also keep in mind that not every user has javascript enabled.