Look at the page in the Space Marine Codex that defines what "and/or" means. Fake edit: Page 128 under "options." Translation: you don't have to replace either weapon, which isn't consistent with other entries in the very same Codex. Things like Sergeants must replace the Bolt Pistol or the Boltgun, and so on depending on what option is being taken, the Captain is not obliged to replace anything.
Two-handed weapons simply can't be combined with a close combat weapon in order to gain a bonus attack. It's a very common convention for a model with a two-handed weapon (a Howling Banshee Exarch with Executioner, a Sister Superior with Eviscerator and Bolt Pistol) to also have a one-handed weapon.
In other Codex books, it also prohibited the model from taking two two-handed weapons. However, that is a Codex-specific prohibition, usually spelled out in the wargear section or above the HQ heading. That restriction is also gone, so the Master can even take a Storm Bolter and Relic Blade. Finally, the limit on how many weapons he can take is gone. If you're taking a Relic Blade and Storm Shield, you may as well get a Storm Bolter too if you have points to spare.
