The MySQL Deprecated Variables issue is pretty straight forward. MySQL doesn’t generally warn you if you use old variable settings rather than the new ones. Also there is no comment suggesting that perhaps these old variables in my.cnf file will be removed at some later stage. A bug report is already filled. Until MySQL 5.5.21 my.cnf uses both old, deprecated and new variables without a warning on startup.
MySQL Deprecated variables -> new variables
thread_cache -> thread_cache_size
key_buffer -> key_buffer_size
table_cache -> table_open_cache
log-slow-queries -> slow_query_log