If we assume the company runs N projects with positive Net Present Value (NPV) at the start of the project and after re-evaluation some of the project NPV turned to be negative, closing the project and laying off the staff will actually make company worth more.

Yes, but the reason you will see companies put out press releases explaining layoffs is because the market does not on its own make such generous assumptions reliably when it sees layoffs.

(And even if it does, the fact that the NPV of a project "turned negative" indicates that the value of the company dropped, and the layoffs are only a partial mitigation, which still hurts the perception of the company if the market hadn't discovered and priced in the drop before the company did and reacted with layoffs.)

Layoffs are a signal that a company feels they don't see a way to get a high enough ROI on their productive capacity. That could be performance related, or it could be e.g. that the company does not see good R&D avenues to pursue, so they scale down their R&D org. Or market demand dries up so they scale down their sales org. Or interest rates change, changing the definition of "high enough ROI". In theory people working in computer fields are always building automation so it should be easy to scale down and coast in maintenance mode if the business wants to do that. That applies less to video games of course, but even there the top selling games each year consistently feature Call of Duty <current year>, Madden <current year>, and FIFA <current year>.

Layoffs indicate a poorly run, inefficient company, especially if other companies in the same industry had fewer layoffs. Typically this means that the company hired and trained more workers than it needed; their estimates of future opportunity was wrong relative to other companies that did not require layoffs because they’re hiring was based on more accurate estimates.

Another factor is that retained employees that learn of companies layoff frequently become concerned about their own position and the treatment of the workers that were laid off, reducing employee morale. High performers may start looking for another job in order to avoid expected future layoffs.

Then there’s the impact on potential future employees, who will also know about the layoffs. These employees will be aware of recently layoffs and will expect more money from said company who will also have to train the new employee that replaced the one they laid off before.

Finally, you have the impact on potential customers or existing customers. Some customers have relationships with employees that are laid off, and this can be jarring. The customers may become concerned about the liability of the company or the management of the company, potentially moving all our part of their business to another firm.

All of these effects are not typically beneficial to the company or it’s shareholders.