That's up to you. What that does is sets the number of lines in every window that you can scroll through. Most people really don't need to scroll back 1000 lines. If you keep logs of any important channels then lowering it isn't a big deal. Or, if you just don't care about stuff 1000 lines ago, you can lower it as well. Keep in mind that the setting affects every window, though. If you need that much scrollback for even 1 window, you shouldn't lower it. You can "bypass" that setting in a window by scrolling back a little and leaving it there. Doing so will let the channel accumulate all lines into the buffer until you return and scroll back to the bottom. This can let you keep an entire window's text while you're away so you can scroll back through all of it if you want a lower buffer and don't want to lose a higher buffer while you're away on certain windows.
In the end, it's completely up to you. Whatever works best.