Only if they change the template, and even then, you have the choice of changing the template yourself, or having the new template write over your custom template, i think 4 templates were changed from beta1 to beta2, i doubt may more will be changed for the release version.
Any templates that you have added or customised through the regular systems (the standard control panel or my replacement control panel) will stay the same when you upgrade to a new version.
Any hacks that require you to make alterations to the .php files will need to be re-installed, usually following the same instructions that you used to install them in the first place.