Papers published in journals which are not indexed by SCOPUS or Web of Science, are not considered for the national assessment of researchers or laboratory performances in many countries. It thus would be much more interesting to publish in journals indexed by SCOPUS or Web of Science, or both . Otherwise the quality of their content may be subject to caution.
This question might overlap with the interest to publish in open-access journals, which for many of them are not indexed, - mainly because they prevent the leaders of edition from some money. Among these open access journals, there might be some good journals, but they are still considered with caution due to the situation in regard of major indexation sites.