src: use non-deprecated Get/SetPrototype methods

nodejs/node#59671

Co-authored-by: Shelley Vohr <shelley.vohr@gmail.com>

Author: trop[bot]

patches/node/.patches

@@ -39,7 +39,6 @@ fix_array_out-of-bounds_read_in_boyer-moore_search.patch
 test_accomodate_v8_thenable_stack_trace_change_in_snapshot.patch
 chore_exclude_electron_node_folder_from_exit-time-destructors.patch
 api_remove_deprecated_getisolate.patch
-fix_replace_deprecated_setprototype.patch
 fix_redefined_macos_sdk_header_symbols.patch
 src_simplify_string_bytes_with_views.patch
 src_improve_utf8_string_generation_performance.patch