public function countPublicProductsByCategory($categoryId)
{
    $qb = $this->createQueryBuilder('p')
        ->select('count(p.id)')
        ->innerJoin('p.ProductCategories', 'pct')
        ->where('pct.id = :categoryId')
        ->andWhere('p.Status = :status')
        ->setParameter('categoryId', $categoryId)
        ->setParameter('status', ProductStatus::PUBLIC)
        ->getQuery();

    return $qb->getSingleScalarResult();
}

/**
 * @ORM\Column(name="product_count", type="integer", nullable=true)
 */
private $productCount;

public function getProductCount()
{
    return $this->productCount;
}

public function setProductCount($productCount)
{
    $this->productCount = $productCount;
}

public function updateProductCount($categoryId, $count)
{
    $category = $this->find($categoryId);
    $category->setProductCount($count);
    $this->em->persist($category);
    $this->em->flush();
}

class UpdateCategoryProductCountCommand extends Command
{
    protected static $defaultName = 'eccube:update-category-product-count';

    protected function execute(InputInterface $input, OutputInterface $output)
    {
        $categories = $this->categoryRepository->findAll();
        foreach ($categories as $category) {
            $count = $this->productRepository->countPublicProductsByCategory($category->getId());
            $this->categoryRepository->updateProductCount($category->getId(), $count);
        }

    }
}

bin/console eccube:update-category-product-count