I think that
Frederick and
Deborah are pretty similar, pronunciation-wise. Usually they are basically two-syllabled, but for special emphasis (Fred-er-ick, tidy your room or I'll throw all your mess away! Deb-or-ah, finish your cabbage, there's nothing wrong with it!) what is otherwise a neutral vowel hardly pronounced at all becomes a fully fledged syllable.
And so, since
Fredrick looks like a spelling error and will lead to constant explanations for as long as its owner is alive, I would use the traditional spelling, in which the second e isn't 'extra' at all, it's historically accurate.
It is a good name! Given enough sons, I'd have seriously considered it.
Freddie is fine on a small boy, but it will become
Fred later on, which is also fine. Plus, if you leave the second e unmolested, he might choose to become
Derick!