[r/python] Deprecation notices for used_shape

[johnkerl]

Issue and/or context: For #2407

Changes:

Notes for Reviewer:

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 90.22%. Comparing base (c931ffe) to head (8cdaef9).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2834      +/-   ##
==========================================
+ Coverage   90.06%   90.22%   +0.15%     
==========================================
  Files          37       37              
  Lines        3937     3940       +3     
==========================================
+ Hits         3546     3555       +9     
+ Misses        391      385       -6     

Flag	Coverage Δ
python	90.22% <0.00%> (+0.15%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	90.22% <0.00%> (+0.15%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

Not related to this PR. Lint flared up today right here. IDK why.

[mojaveazure]

For the R API, you could also call .Deprecated() in used_shape() to throw a deprecation warning when calling that method

[johnkerl]

We have some flakiness around (I think) the particular linter version available -- something bumped today -- lint passing on Python 3.8 and failing on Python 3.11, and it appears they cannot be both appeased simultaneously ...

[johnkerl]

For the R API, you could also call .Deprecated() in used_shape() to throw a deprecation warning when calling that method

Oops @mojaveazure I meant to do that on this PR -- I'll put up another