Most bottom bracket shells have at least one 5mm threaded hole to allow a bottom bracket cable guide to be bolted on so it's obviously not a problem if you add a second one that size.

As to a cratridge bb, grease the shell and threads just to prevent superficial rust. Water won't get to the bearings.

BTW, there were plastic cylindrical sleeves commonly used with cup-and cone bottom brackets. They were sandwiched between the cups and covered the bearings and spindle to provided a measure of protection from dirt and water.