Blocking .DS_Store files (and ._.DS_Store) is safe -- they contain information from the Finder about how a folder was displayed (icon vs. list vs. column view, icon positions, etc). Blocking other ._ files are only mostly safe. They store filesystem metadata about the files, including resource forks (if files have them, but it most don't), Finder tags, quarantine info, ... lots of things. In most cases, this metadata is unimportant, so blocking them is mostly safe.
But there are a few cases where this info is important; the most obvious is Finder alias files, which break completely without the metadata (in this case, it's actually type and creator codes that're critical). The simplest rule is that if a non-Mac computer (Windows, unix, linux, etc) could use the file, killing the metadata should be safe. But if you're using any Mac-only stuff (e.g. Finder aliases), it might not be.