I would’t be affraid of wp_enqueue function itself, not PHP slowdown. But enqueuing more javascript files really matters. But not from the PHP point of view. Each website (even in pure HTML) is getting slower with each other request till it brings all the files. The firs request is HTML file (that’s why we use gzip compression for this file), next requests are for CSS and JavaScript files, images, flash components and other stuff.
For CSS and JavaScript we have got a minifiers for JavaScript and CSS and that’s why we use CSS sprites for multiple images being in just one request. Each request is a slowdown.
I would recomment you a project yslow – to get more insight.
And now back to your question. Merge your JavaScript and minimize it. But keep developer version (mysctipt.dev.js) for future developing and enqueue myscript.min.js to your theme (as WordPress itself does). And ship both of them along with your theme.
And another important thing. If you’ll go round wp_enqueue_script hook with your css, some plugins for automatic minifiing of scripts and CSS wouldn’t work as expected for users of your theme. Use that function.