@Nick are you sorting the files by last modified? That one is particularly slow and soon we’ll add a pop-up to warn you about this.
Also, is it slowing down before the files are being shown or while they’re being shown (and the files appear slowly…)?
If the first case is true, than the slow-down is connected to the sorting by date.
No, we’re not indexing the files, if we did we’d need to grow the db (and use more ram) or to read/write the db from a file (and this is would slow down badly…right now the whole db is alway loaded in memory and it’s written on the disk only to save/back-up.

@mrdna what a keen eye! 😀 This is indeed a part of making the rules engine smarter. This trick (as far as I understand) is used because the engine is waiting for a couple of secs to see if the user renames the file: if the file is renamed within that time, only one pop-up comes up instead of 2 (one for the file with the original name and one for the file after being renamed) which might be perceived as bug. This is useful when you create a file/folder from the right-click menu and then you rename it straight away.