DHCP supersedes BOOTP; you keep BOOTP around only to help old hardware and software which does not know DHCP. Anyway, both are about offering a service to whoever asks (namely, IP address allocation and publication of network configuration) so they are no more, and no less, a security issue than what their definition entails: by running a DHCP or BOOTP server, you make it easy for people to plug in and get network connectivity.
Neither is more secure than the other, but if you offer both then you must mind both when it comes to controlling access to that service (e.g. MAC filtering). See this page for a comparison.
The usual security stance applies: if a service is not needed for operations, then don't enable it. To know if a service is needed for operations, disable it and see what breaks. In that case, deactivate BOOTP, and if you can live without it (which is probable), just leave it deactivated.