Yes, Perl 6 will certainly have eval, and yes, it will certainly disable certain kinds of optimizations--just as it does in Perl 5. That's the nature of the beast. And if you're going to compile a program for your PDA, the size of the executable may grow dramatically if you use eval, since it then has to include the compiler.
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It's just that eval, like goto, is the most general thing in its class. You never want to use either of those when there is a more specific construct that does what you want. Just as we've added various controlled forms of goto over the years, we've looked at the various uses of eval over the years and abstracted out various common operations like aliasing, symbolic references, and closure generation.
As for all the references to optimizations, don't sweat it. It's something language designers and implementors are supposed to worry about, and that concern leaks through at times. But most users shouldn't have to worry about it, at least until they have a bit of code they need to make run faster.