Most of time I imagine it's just fine. However, if your Pre was in the process of doing something unsafe, where it was assumed that the process would complete, then you could have a problem. Good developers avoid getting into this situation, but I'm sure that even Palm has code where things can't be gracefully rolled back.
When the Pre first came out, a Sprint rep on their "buzzaboutwireless" site said that if you remove the battery without a proper shutdown, the network may not receive proper notification of what happened to your device. She said that this could adversely affect the Sprint network (which might flood "where are you?" messages to a device that won't answer) or it could cause your device not to be recognized when you put the battery back (because Sprint, not wanting their network taken down by people removing batteries, will cut you off). Seemed like bunk to me then as well as now.
The bigger issue, I've found, is that in some Pre models, removing the battery can cause the battery to break. The plastic casing around the actually battery has cracked on mine because the battery was in too tight. Sprint's answer (I have insurance): we don't cover batteries and this is clearly you abusing your device, so you'd better go away.
Short answer: if you need to remove the battery, go ahead. At worst, you'll have to recover from backup. Yes, Palm Backup isn't perfect...
Also, if you're still seeing the loading screen after 45 minutes, best to take the battery out again. I've had this happen, where the Palm loading screen never goes away. If I do a battery pull, it then boots up just fine.