There's another thing too. It seems the PS2 is set by default to spin-down the HDD after 20 minutes of inactivity. Software with HDD support may have an option to override the default setting, like FFXI and POL Viewer does. I'va had to pause a game and walk away for about an hour before, and when I come back, it will lag a bit the next time I need to load anything while it spins the HDD back up to start accessing data on it again. I don't think HDLoader has a setting to change that.
My PlayStation2 HDD guide.
NTSC J SCPH 30000 with HDD and PSBBN 0.32
NTSC U/C SCPH 30001R Astral Blue LE PS2
Final Fantasy XI status:
Server - Ragnarok, Race - Mithra, Jobs - BLM 72 WHM 51 SCH 39 SMN 25, Nationality - Windurst, Name - Bungiefan