Repositories for sys_category don't respect storage pids by default. See https://forge.typo3.org/issues/89295#note-10

CategoryRepository.php

<?php

namespace Me\MyExtension\Domain\Repository;

use TYPO3\CMS\Extbase\Persistence\Repository;

class CategoryRepository extends Repository
{
    public function createQuery()
    {
        $query = parent::createQuery();

        // This has to be set explicitly to 'true' due to the fact that sys_category
        // has rootLevel != 0 in its TCA and hence extbase will set it to 'false'!
        // See: extbase/Classes/Persistence/Generic/QueryFactory.php
        $query->getQuerySettings()->setRespectStoragePage(true);

        return $query;
    }

    public function findAll()
    {
        $query = $this->createQuery();
        return $query->execute();
    }