According to its online documentation, the IBM Home Page Reader (HPR) supports ECMAScript/JavaScript. (ECMAScript is the standard. The implementation of the standard is commonly called JavaScript. It is called JScript in Microsoft products). That reader even supports dynamically modified page content (as long as it is done properly using the DOM functions). Note that the ECMAScript communication API used by SCORM, while it requires an ECMAScript implementation, has no visible component and therefore does not affect accessibility. See
http://www-306.ibm.com/able/solution_offerings/hpr4devhelp.html for a very useful page of online help for developers. I have not tried HPR myself, but I'm very interested in hearing about other people's experience with it.