yes the internal drive has an impact on performance. this is related to how much RAM you have, but even if you have the max 2GB RAM that you can have in a macbook (or 3GB if they updated it to that like the pros), OSX still uses the system drive for a great deal of swap files. logic does too. it's just the way it all works. back in OS9 days, you may (or may not) remember a thing called virtual memory.. well that hasn't disappeared from OSX as many people think, it's actually built in and always operating under the hood, but it self-manages... there's no need for a user to assign amounts of hard drive for VM, or to assign the memory allocation for applications. OSX does it all by itself, and it does make judicious use of the system drive just to function.
logic also is part of this equation. depending on how you set it up, if some of your exs library is on the system drive (such as the basic library or garage band sounds), then it's possible that logic will access the sys drive at times if you have exs streaming enabled. also, if your freeze files get created on the sys drive, they'll be read from there too.
with all that in mind, the other thing is that the 5400rpm is not really that slow. in fact, if it is a drive that uses the new PMR technology (the 5400s in the latest macbook pro do use this, don't know about the standard macbook), then there have been plenty of tests out there that show it's almost as fast as a 7200rpm longitudinal drive, and under some circumstances, faster.
personally, I ordered a macbook pro with a 7200rpm because I want my system drive to be as zippy as possible for all the fast read/writes that the system does. battery life is not an issue for me as it will always be used in a powered situation. a good review of the 7200rpm drive vs the new PMR 5400s that are the options in the new macbook pros that I read on the net said that the 7200 still does have the slight edge in performance. except, curiously, when the drives are both getting full, at which point they both slow down and the 5400 almost equals the 7200. I wish I could remember the site so I could post the link, it was a laptop review site and they ran their own tests so it wasn't just based on quoted specs.
anyway for me I'm still going to use an external FW800 for audio and sound library, the internal is just for system. I made the choice to go 7200 for the system performance reasons above, but I really don't think you'll be disappointed with the 5400.
