Theme options panel in wordpress. Best practices

Most free and premium themes offer a theme options panel. Most of them use a $options array to store the options and after that, they just get the options when needed.

From my point of view, using lots of options may increase the mysql load and the number of queries. Wouldn’t it better to serialize the whole $options array and then to retrieve it in the header, having access to all the options with just one query?

I need some advices on which one is better and for some other practices around this issue.