What do you call the additional money you pay when you buy a store or restaurant in return for many cutomers and nice facilities?

Goodwill may be a term that you are looking for:

"The goodwill amounts to the excess of the "purchase consideration" (the money paid to purchase the asset or business) over the total value of the assets and liabilities."

More generally, you seem to be talking about the intangible assets of the business, if you're defining "extra" as anything beyond the funds paid for the physical facility (as suggested by focus on the cost of building the store).

You could also be talking about the capital gain or appreciation in value, which would even apply to the real estate itself being sold for more than the $100K it cost to build. Appreciation is more a result of rising prices of comparable assets, while the term "capital gain" leaves open the possibility that it may be more resulting from active efforts of the owner.

Economically rational sellers will generally sell for as much as they think the market will bear (i.e. as much as they think they can get) regardless of the resources they originally put into it.

There isn't really a specific word for this in English. In general, the value of a business is not just the value of the building, fixtures, and fittings; a successful business simply has a greater value than an unsuccessful one.

You might apply tangible¹ and intangible² as this page does:

Although there are relatively easy ways to value certain parts of the business – such as stock, fixed assets...there will very probably be a sizeable intangible element to the value of a business.

In business terms, this kind of valuation is called an income valuation (as opposed to liquidation valuation) because it presupposes that the business will continue operating.

¹ tangible "able to be touched or felt" - Merriam-Webster

² intangible "not made of physical substance : not able to be touched : not tangible" Merriam-Webster

If you're buying a company then the value of that company is factored into the price, usually some multiple of the yearly revenue. The specific multiple is determined by industry and often by credit agencies. The total value of the company, the valuation, therefore includes the physical and financial assets, as well as a measure of how much money it is expected to make.

If you're merely buying a property then the value of the company that inhabited that property is not considered meaningful, except insofar as it increased the inherit value of the property (through, say, fame), which in turn is a factor of what people are willing to pay for it. Such factors are usually called a markup. If the markup is high relative to similar properties, you are said to buying at a premium.

Notably any money you make on a property past what it cost you is simply called profit. All value is embedded in the property itself and is not differentiated between base cost and "tip".