I asked this same question back in I think 2009 or so on Macroquest2.com. I received the same answer. However, I'm ultra paranoid and don't add anything to hotkeys these days. Between /alias and CustomBinds, I'm pretty well set. This way when MQ2 is down, all my hotkeys still 100% function and I can continue to box on my own.
Additionally, this allows more of a variable and dynamic playstyle. For example, I could create a hotkey on one character that said something like /bcg //nav id ${Me.ID}. But I could only do that on that character. I could create a hotkey on all 6 of my boxes (assuming I only have 6 characters I ever play). OR I could create an alias of /mup /bcg //nav id ${Me.ID}, bind that to Shift + M, and then I could simply press Shift + M on any character, any screen, or any PC (my MQ2 is installed and shared on my personal dropbox so when I make one change somewhere, it propagates to my several physical boxes).
What I'm NOT saying is, "don't use hotkeys". Contrary, use hotkeys all you like. What I AM saying is "Aliases and CustomBinds are also a valuable resource and if you don't know how to use them, research them or ask about them; then decide if you'd like to incorporate those into your game."