I think this is just handled by the setting of the variable 'lock_wait_timeout' :
It is true that some backup tools will LOCK (complete) tables. This applies to some backup tools deployed on various hosting systems and integrated into various 'Control Panel' applications But IMO this just reflects that the still think MySQL is == MyISAM (because wiht MyISAM etc. there is no other way to ensure consistency). With InnoDB you may 'backup in a single transaction'. mysqldump (
http://dev.mysql.com/doc/refman/5.1/en/mysqldump.html#option_mysqldump_single-transaction) and also other tools support this (at least SQLyog/SJA does).