Yes, it's considered "old stuff," and it will run noticeably slower than a 7200 rpm drive. It'll be slower opening programs, slower saving data, slower to load at start-up, etc. I'm typing away right now as a matter of fact on my mom's old Gateway computer from 1998 and it has a 5400 rpm Western Digital hard drive. It's slower than molasses. Takes like 5 minutes to boot up in the morning. Running a virus scan takes an hour (and there aren't that many files on this computer!). A de-frag takes a good 30 to 60 minutes as well. It's pretty noisy too. On the plus side, it's worked flawlessly for exactly 6 years now.
It would be a shame to put a 5400 rpm drive with that nice chip & RAM you're getting. That "bundled" hard drive is prolly one that someone's just tryin' to get rid of and get a few dollars for. If it's a "throw-in," you might just take it anyway (and keep it for a back-up or something), but I'd buy a new 7200 rpm Seagate or Western Digital HD to actually use as your main drive. (Incidentally, Seagate now offers a 5-year warranty on their 7200 rpm drives, which as of a few months ago [last time I checked] was unmatched by any other company. WD offers a 5-year warranty on their 10K-rpm Raptor, but that's a different animal. 😀 )
You could always install 2 HDs, of course, and use the 7200 rpm one for programs and the 5400 rpm for extra storage. Better than having it sit in a box on a shelf or something.
That's my two cents. Hope you find it helpful. 🙂