They are not subcommunities. They are partially intersecting communities. Many of the questions on Database administrators are firmly on the database side, involving no administration at the system level. Most questions on Webmasters involve the page contents, not the administration of the servers. Many of the questions on IT Security are not about system administration but about application security, data security, etc. The list goes on and on.
This is natural: subjects intersect, audiences intersect. You can't have a straight separation between subjects. This happens in fields that aren't computer-related as well; for example there's a science fiction site which discusses SF books and movies (and, occasionally, SF in other media).
Across the Stack Exchange network, I'm only aware of a single case of a site whose subject is a subset of another site's: Ask Ubuntu, where all the questions would be on-topic on Unix & Linux. You'll note that AU has a lot more traffic than U&L. A significant proportion of AU users don't care that there are other Linux distributions (let alone unix variants); they want an answer for their computer. They wouldn't be as satisfied with U&L answers, which often tend to be more generic at the expense of being more complex.
Grouping sites doesn't work in all cases. AU vs U&L is an example: AU superficially looks like a tag on U&L, but the target audiences are different. Beyond content, there's also the issue of moderation policies: they are not the same on every site. For example, circumventing someone else's policy is a big no-no on SF, only raises a few eyebrows on SU, and is not a concern on U&L. Different sites have different stances on “soft” questions such as literature requests or social concerns. Again, tags don't allow such differenciation.
On practical matters:
- If you wonder where to ask your question, think which community is really focused about that subject. If it's primarily a system administration question that happens to be about a security feature on Linux, ask on SF. If it's a question on security that happens to be about a Linux feature, ask on Sec.SE. If it's a Linux question that happens to concern a security feature, ask on U&L.
- If you have cross-site interests, which is inevitable for many people (for example, you can guess from my profile that my interests include various computer-related topics as well as science fiction and French — they aren't all going to be on one site), create a tag filter on
stackexchange.com. - Reputation denotes expertise in a particular topic (insert caveats here). That's why it's per-site.
