It feels relatively easy because your employer takes care of the calculations and the consequences of your personal situation are sorted out later. But at the end of the day, the structure of the income tax is not particularly simple. Even without taking all the credits and deductions into account, the rules for employers fill a 300+ pages manual.
The general idea behind the system is that if you paid too much, you get it back at the end of the year. Same thing for all the deductions. So if you stop working during the year or have a large mortgage, you can get quite a bit of money back at the end of the year. But your employer does not take it into account to compute the monthly withholding so the answer to the “How do they calculate it in this case?” question is “They don't!”.
If you anticipate a large discrepancy in one direction or the other, you can however ask for a “voorlopige aanslag” (or “provisional assessment”). You would then receive money monthly, with the remainder to be paid later, after the final assessment.
Finally, if you your income fluctuates a lot from year to year, you can also ask the tax office to smooth it over three-year periods and to recompute the income tax accordingly. It can mean that money taxed in a higher tax bracket in one year gets moved to a lower one because you did not go over the threshold in another year, thus reducing the overall amount you have to pay. This is called middeling sterk wisselende inkomens.
Beyond that, the tax code makes liberal use of deductions and credits to define complex rules so that the notion that there are only three straightforward tax brackets might be a bit misleading. Where the German tax code has different tax brackets and/or rates, the Dutch tax code has a seemingly simple set of basic tax rates modulated by these deductions/credits.
As an example, consider the algemene heffingskorting. It's a tax credit between €700 and €2000 that every taxpayer gets (hence “algemene”). Because everybody qualifies for it, it means that the first €XXXX of income are effectively tax free (akin to the German Grundfreibetrag and similar rules in many countries). But it's not described in that way, you first compute the income tax based on the usual rates and then discount the credit (in German this is typically called an Absetzbetrag).
Then to make everything more complex, this tax credit varies depending on your age, your income or whether your partner earns money. And some of the rules (e.g. on fiscal partners) are being phased out and only apply to people who benefited from them in the past. So there is a lot more complexity in all this than meets the eye.