I think there might be a small benefit to using DOS if you are using compact flash or an SD card for storage. Windows 98 would be expected to write to the hard drive more, so you wouldn't expect your card to last as long. Personally, I've never had to replace a CF or SD card in a Windows 98 machine, so it's not a big concern for me. Moreover, CF and SD storage is dirt cheap, so I'm not worried about cost. I've seen some people suggest that you should set "ConservativeSwapfileUsage=1" to preserve your storage longer, but I've seen others say it does nothing.
Someone more knowledgeable than me could probably give you a better idea if booting into pure DOS would save any wear and tear on your storage. I don't know how often Windows 98 uses the swap file, especially if your just gaming. Another question would be if Windows 98 writes much to disk when it is starting up or shutting down. If it does, it wouldn't surprise me if constantly rebooting would actually decrease the lifespan on a CF card.
All that aside, I prefer to set my Windows 98 systems to boot straight to DOS anyways. I use Linux for work, so I feel at home on the command line. If I need to run a program with command line parameters, I just need to type them in. I also find it quicker to navigate between different directories. I also don't have to make room on my desk for a mouse unless I'm using a program that needs one. I only use Windows 98 if a program needs it or if I need to copy a file from a USB stick. For me, booting straight into DOS is more convenient and I just need to type Win to launch Windows.