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Answer of your question
1. wordpress tables are highly optimized and we can use all core functions for those tables. You can google, you will find hundreds of reasons to use wp table.
bbPress uses wp tables. wordpress.org use bbPress as their support forum. Do you think you have more users and more messages then that support forum?
2. it is always better to use equal ( = ) query then LIKE query. we can easily use equal query if we use duplicate meta_key. Also wordpress support duplicate meta_key. So if your custom coded message plugin shows error for this i think you should change code of that plugin so that it does not show error.