There are different types of ships in Eve:
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Capsule ships with crew. The article link provided by Geo Eclipse gives good information to support this. It is also referred to in other lore articles. For example there is one story where a regular crew member sympathizes with the target his capsule-captain is attacking. He then sabotages the ship he is on, resulting in the destruction of the ship and death of most of the normal crew.
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Capsule-only ships. There is a graphical book that CCP published with 3d-cutaway drawings of some Eve ships. Small ships, for example the Republic Firetail, is shown with a capsule only, and no crew. (There is also a Gallente ship with a capsule and no crew… but it has dancers and a dancing pole… heh)
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Capuleer with AI assistant. Aura assists capsuleer pilots, and according to CCP she is is a ‘weak AI’ not capable of learning. However, she can do a few tasks on her own including warp, get docking permission etc. AI assist can be found on ships with regular crew, and also without crew. So it kinda fits in both of the 2 above categories. (https://universe.eveonline.com/lore/aura#technology)
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Non-capsule ships with regular captains and crew. There are references to this in various ingame places. For example: In the Sisters of Eve epic arc you have to destroy a frigate ship piloted by Mizara - she is a regular person and not a capsuleer. At the end of the one branch in the Amarr epic arc there is a battleship is piloted by Harkan, who is not a capsuleer. He even makes a few snide remarks about capsuleers. (In contrast in the same arc there is Rahsa, which is a NPC and a capsuleer.) Tom’s shuttle is another example of a ship piloted by a non-capsuleer. He died long ago, but his ship keeps floating through space and pops up in random places.
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Automated AI ships with no human pilot. The Orphyx, Rogue drones, and Sleeper ships are examples.
A short description about the function of crew on capsuleer ships can be found in this article from CCP:
https://universe.eveonline.com/lore/ship-technology#internal-functions
Capsuleers control some aspects of ship operations, and can even push their vessels into overdrive when necessity calls.
Beyond that, though, operation of space vessels is a complex and tricky endeavor that requires the combined efforts of often large groups of experienced people.
So ships have crews, and some concessions need to be made to their comfort and well-being onboard their respective vessels. Those crews are thankfully not lost when the ships are - well, not all of them, at least - and thus can build up the experience needed to run the various internal systems that are either unreachable by or beyond the interest of capsuleers to focus on.