For SEO reasons. See https://support.google.com/webmaster...er/76465?hl=en
By getting thin, low quality and/or duplicate content pages (= your store pages) indexed you will drag down the overall "quality score" of your site considerably.
That's why your site can be caught under some sort of Google Panda penalty - which is a domain-wide penalty (meaning all of your pages will suffer as a consequence).
You want to ensure that only valuable, high quality, unique pages on your site get indexed in the search engines.
Therefore - even with 2000 to 4000 products - I'm suggesting to noindex all store pages (unless you don't care about Google and plan to drive traffic to your site via other ways).
To noindex your ENTIRE store (store home page, every store category page and product details page) make sure that you add a <meta name="robots" content="noindex"> on the following pages in the Factory:
The Factory > Your Store > VIEWS > STORE FRONT PAGE > Default > View menu > View <head> Elements
The Factory > Your Store > VIEWS > CATEGORY PAGE > Default > View menu > View <head> Elements
The Factory > Your Store > VIEWS > PRODUCT DETAIL > Default > View menu > View <head> Elements
Then plan and add unique content (product reviews, how-to information, ...) to your site on a regular basis and try to rank these unique content pages leading visitors this way into your store.