Encryption stores used key_version to
FIL_PAGE_FILE_FLUSH_LSN_OR_KEY_VERSION (offset 26)
field. Spatial indexes store RTREE Split Sequence Number
(FIL_RTREE_SPLIT_SEQ_NUM) in the same field. Both values
can't be stored in same field. Thus, current encryption
implementation does not support encrypting spatial indexes.

fil_space_encrypt(): Do not encrypt page if page type is
FIL_PAGE_RTREE (this is required for background
encryption innodb-encrypt-tables=ON).

create_table_info_t::check_table_options() Do not allow creating
table with ENCRYPTED=YES if table contains spatial index.