https://investinestonia.com/business-in-estonia/taxation/
Estonia's corporate income tax rate is not essentially zero, unless you plan to never distribute any profit. Otherwise it's 14-20%. It would be unusual for most businesses to never distribute profit.
Last year Estonia collected something like €368m in corporate income taxes. Or €283 per capita. Equal to about 4% of their budget. Not a huge sum, also not anywhere close to zero. In the US for 2018, corporate income taxes will be about 5% to 6% of tax revenue (4% to 5% of the budget). The US corporate income taxes collected, broken down on a per capita basis, will be around $650 to $700 for 2018, for comparison.
You can plainly see that Estonia collects corporate income taxes:
https://www.oecd.org/tax/revenue-statistics-estonia.pdf
The primary unusual thing Estonia does, is not tax profit until distribution.