The same reason you unmount (or "safely remove" in Windows) your pendrives on computer. User may not have any app opened, but there might be some system deamon (like tracker indexing multimedia files) or some delayed write operations may be performed (I don't know how it works on N900, but often when you want to write some files to your pendrive on your computer, the system may show that operation finished, but the driver is still packing it on the device and writing and thus using it). And if one would take sd card out of reader, it could lead to memory corruption and loss of data (the same applies to removing pendrives from your computer without using "safely remove" option :P)

Well, how often DO you change boot? It flashes kernel only when you actually select different option than previously (if you choose the same kernel as previously, it looks inteligent enough not to flush it again). So, if you don't have multiboot and thus only boot one kernel, your nand would be safe. And if something would go wrong, you could just choose second (fail-safe) boot option, for example the default omap1 N900 kernel. I think that, after all, this means the same or less write operations to nand than using flasher on your pc, am I right?