The ‘tree’ object, representing directories in Git, stores file name and (subset of) permissions. It doesn’t store inode number (or other kind of file id). Therefore hard links cannot be represented in git, at least not without third party tools such as metastore or git-cache-meta (and I am not sure if it is possible even with those tools).
Git tries to not touch files that it doesn’t need to update, but you have to take into account that git doesn’t try to preserve hardlinks, so they can be broken by git.
About symbolic links pointing outside repository: git has no problems with them and should preserve contents of symbolic links… but utility of such links is dubious to me, as whether those symlinks would be broken or not depends on the filesystem layout outside git repository, and not under control of git.