Should computer science indexing sites be considered in rating research? I am currently working at a university of applied sciences, in the field of Computer Science. Recently there has been formed a section that is in charge of giving stipends related to research. This group has put as a rule that they will only fund research that is indexed in Scimago and in Scopus, but that this could change over time. They have in mind that this would help the institution for increase their visibility in terms of research.

My question is, for our field, should there be other criteria considered, such as if the publication has been indexed in ACM, IEEE Xplore, or DBLP? I mean, there are some conferences that are not considered in Scimago or in Scopus, but that have a good reputation. How to propose that change? What do you think about considering these indexing venues also?
Computer science is typically badly under-represented in the "traditional" citation indices, which do not consider conferences to be peer-reviewed publications.  As any computer scientist knows, that is a bad joke: many computer science conferences are much more stiffly reviewed and difficult to enter than most journals.  

It is for this reason that DBLP was created, to actually index relevant and reputable computer science publications.  I believe that DBLP should cover everything in ACM DL and IEEE Xplore, so getting just that accepted by the university should be sufficient.

Unfortunately, what you are seeing is another instance of a long-running and frequently waged fight.  Take heart, however, that this fight has already been won at most top institutions, and can be won at yours as well.