If I consider changing my WordPress DB tables to InnoDB, will it have an effect on the way WordPress works?

There’s quite a lot of information on here about switching to InnoDB

https://wordpress.stackexchange.com/search?q=innodb

There are a number of things to think about:

  • InnoDB is helpful with you’re faced with contention – ie when you have tables that are being written to as well as being read
  • InnoDB does not support FULLTEXT indexes so plugins that rely on that will either break or work slowly.
  • You can choose which tables to convert to InnoDB – it’s not an all or nothing deal – on some of my sites, wp_comments is the only table that’s InnoDB because of the massively bursty nature of comments on those sites.

However, it sounds like you’ve got more fundamental issues that need to be sorted out before you worry about switching to InnoDB.

  • you really need to log your slow queries and then EXPLAIN them to understand what’s going on – you might just need to optimise tables or add additional indexes – it’s quite likely that some of your plugins are executing queries that are forcing sequential searches on your database. Find out and add indexes to speed these up, if that’s the case.
  • Once that’s done, you can then look at optimising Apache or switching to a more advanced setup (eg nginx + PHP-FPM).
  • Check your caching. If the site isn’t changing much, most content should be served up from the cache instead of hitting the database. Find out why this isn’t happening.

In short, it doesn’t feel like you’ve really got to the root causes of the problem. Until you get a better handle on that, anything you do is going to be a bit random.