[r] Replace `vfs.is_dir` with `SOMADataFrame::exists` et al.

[johnkerl]

Follow-up from merged PR #2704.

As discussed in detail here: https://github.com/single-cell-data/TileDB-SOMA/pull/2704#discussion_r1635386307

• A VFS is-dir check -- in R, Python, or C++ -- will work for local-disk and S3 URIs but not tiledb://... URIs
• exists -- in R, Python, or C++ -- is the method within the SOMA API that works regardless of storage backend. It does not assume VFS.
  • In libtiledbsoma, these are SOMADataFrame::exists, SOMASparseNDArray::exists, SOMADenseNDArray::exists
  • As noted at https://github.com/single-cell-data/TileDB-SOMA/pull/2704#discussion_r1635386307 we intentionally do not unit-test tiledb://... URIs within this open-source repository.

cc @eddelbuettel @nguyenv

[eddelbuettel]

Done in #2803