I've primarily been working with Microsoft SQL Server for about a decade and I've never heard of the term "memory fragmentation". First result in Google quotes it as "Fragmentation of memory is a memory disorder where an individual is unable to associate the context of their memories...".
Kidding aside, I'm not aware of any specific memory issues with querying the system entities in SQL Server, but I would say the following are potential issues that can occur:
Querying them frequently requires server resources like any other entity, and theoretically could add up, especially depending on the system entity and how efficiently it was designed / coded. CPU cycles, memory, and disk I/O typically being the resources consumed.
Querying certain system entities too frequently could theoretically result in them being blocked, and / or your query on them being blocked and waiting a while to complete. The latter isn't necessarily a problem as much as it could be an annoyance unless you encompass querying those system entities as part of a larger workflow.
Personally, I'm querying certain system DMVs and logging them to a table every 10 seconds, 1 minute, and 10 minutes depending on the system entity and information I want to log, so that I can retroactively troubleshoot performance issues. 10 seconds is probably excessive for most people, and even every 1 minute might be unneeded in a lot of cases, but I like having that level of granularity and it works well in my current system that I support. I have yet to encounter either of the aforementioned issues.
Your mileage may vary on other database systems, depending on the system entities you query, your frequency, and the busyness of your server.