Wordpress Codex says:
Think very carefully before adding a table because it adds complexity to your plugin that many users and site builders prefer to avoid.
Why is it so? Adding more tables is so expensive in wordpress? If so, what are the bad effects of it?
Custom tables can simplify your code, improve performance and help avoiding conflicts with WordPress’ schema changes in the future. Don’t hesitate to use one if you need it.
The extra complexity comes from two other factors: maintenance and multisite.
Maintenance: manual or automatic backups might omit custom tables, so there is a tiny risk that the data in custom tables can get lost. That’s up to the administrator of these sites, it cannot hurt to point that out in your readme.txt and plugin page.
Multisite: If you add a custom table in the main site of a network, there is no way to detect per code whether this table is meant to be a network table (like the users tables) or a site table (like the posts table). WordPress’ naming scheme just doesn’t offer a distinction. This is a problem when you want to duplicate a site in a network per code. So again, your data might get lost during that process.
There isn’t much you can do about that. Some cloning plugins offer hooks to include custom tables. You have to add support for those hooks in your code. So in this case, the extra complexity is on your side.
In fact, adding db table is not very much that expensive as you think. If you configure it well. Suppose, before you create the table it is really you need it. If so, you just need to follow up wordpress database creating table standard. They have their guide line. Another thing to note, you database table never ever should hurt wordpress core functionality. If you uninstall your plugins how you just need to configure your database tables. If you could handle it well, I could also fly with wordpress default SQL for your database tables. Good luck in creating new tables :)
