Yep, they remain there as INE keeps a historic. Take a look at the CSV file, you'll see that the next-to-last column is SUPRIMIDA_INE (deleted in INE).

For instance, 07054000407 (https://www.openstreetmap.org/node/5169959769) was deleted in 2015, and the population data was integrated to the remaining entities. Since then, no more updates has received, therefore, population data is out of date.

This procedure is quite usual when there is a separate residential area, and, over the years, due to the urbanization, becomes closer and closer to any place more important. What the INE does then, is about removing the original value they set, and merge the values.

That's the reason these references must be removed, somehow, they become deprecated. Each year, the INE releases a new file, updated values, new entities and old ones also.

I hope you understand.