Very good question.

Let's break it down:

> A bank give a Merry loan of 100,000$

Concretely, the bank records an asset of 100,000 (the loan) and a liability of 100,000$ (the amount recorded in Merry's deposit account)

> Merry buys a house with this money. 

Analyse it in detail: Merry finds a supplier, who implicitly trusts the bank, who probably as an account at another bank (though not necessarily), and agrees to accept payment in the form of a bank liability. Merry initiates a bank transfer from MerryBank to SupplierBank. MerryBank decreases its liability to Merry by 100,000, keeping only the asset, but adds a new liability to SupplierBank. SupplierBank records an asset of 100,000 (MerryBank's liability to SupplierBank) and a liability to Supplier of $100,000. 

> For a period of 1 year, Merry has paid back 10,000 to the bank. 

Yes, in 99% of cases in the form of bank transfers from other newly created debt from other banks. These become assets in the books of MerryBank (liabilities from SomeOtherBank) and the loan asset is reduced. So while MerryBank gains a 10k asset from SomeOtherBank it actually cancels 10k of loan asset, so its position has not changed - only its risk position.

> Afterward Merry's finance condition worsen and she no longer can pay
> her debt. So in theory, if all the bank borrowers end up in the same
> situation as Merry did, the bank is going to bankrupt.

No. The bank still has an asset of 90,000$ and will use debt collectors to take Merry's property. The bank will then cancel the 90,000 loan asset and record a property asset at market value.

> But if the bank never had the loan money in the first place,

Yes. Fractional reserve requirements for loans was/is often 0%.

>  every penny received from borrowers is a pure profit. Even if Merry returned
> only 10% of her loan, the Bank still profits 10,000 because the given
> 100,000$ to Merry were not bank's money in the first place.

No. See above. The asset position is unchanged. It is a capital increase yes.

> This leads me to the question: Why do banks put interest on top of
> this fraud? And what prevents banks from putting huge amount of money
> to some people's account (for example to the Bank's CEO )? This black
> magic is not quite clear to me.

Interest rate is primarily determined by interbank lending rates to cover reserve and capital requirements. 

I don't know if it applies to the rest of the world, but the main source of income for banks where I live is actually transaction fees. 

Banks could be pure digital banks that have a employees in the hundreds. Typically they are dinosaur institutions that employ in the 10s or 100s of thousands of people. The banks use fees and interest to cover the cost of employees mainly.