Naive questions about the Engine of a Formula1 Car

What are the differences between the two engines (and cars of course). Why a V6 with 1,6L can produce 1000 hp, while the BMW engine (6 cylinders, 3L) produces the half of Ferrari's power?

The basic difference is that Formula One cars have one design purpose: to be as fast as the regulations will allow. Road cars have a lot of other considerations that prevent them from using such advanced, powerful engines:

• Road car engines are built to last - a well-maintained car can easily rack up a six-figure mileage. F1 engines, however, only have to last for a few races - and back in the day, they used the change the engine after every race - so they can crank the power right up. It doesn't matter if the engine will destroy itself after 5,000 miles, because it's not going to do that many miles.
• Because road car engines are intended for mass production, they need to be as cheap and simple as possible, so they can be churned out by the thousand and then sold at a profit. This isn't a problem in F1, where teams only need about 6-10 engines for an entire season, and money is no object. As a result, F1 engines are able to use all kinds of exotic materials and construction techniques that would be impractically expensive even for the most advanced hypercars. (As a benchmark, the Bugatti Veyron required an 8L W16 engine to match the power of an F1 engine, cost $1.7 million, and still sold at a net loss.)
• By that same token, road car engines are designed to run on the fuels you get at petrol stations, and the oils you get at hardware stores. F1 engines use bespoke fuels and oils, from which they can extract considerably more power.
• Perhaps the simplest explanation is that the M3 doesn't need 1,000 hp. What it has is sufficient for its purpose. F1 cars, on the other hand, need as much power as possible, otherwise they're not going to be competitive.

I know there is a substantial difference in weights (more or less 900 kg) and I think this is very important, isn't it? However, is it the crucial point?

The weight of a car doesn't affect the power output of its engine. You could fill the SF90 with ballast until it weighed the same as the M3, and it would still produce 1,000 hp. However, weight is indeed an important factor in the performance of an F1 car. A lighter car with the same amount of horsepower will accelerate faster down the straights, and be more responsive while cornering.

I won't go into too much detail about how F1 cars manage to be so much lighter, but it's essentially for the same reasons listed above: road cars have a lot of requirements (including such trivial things as multiple seats and airbags) that prevent them from being anywhere near as light as a shrink-wrapped, carbon-fibre-clad F1 car.