Devi:

The answer is simple and well stated by others, but I'd like to rehash it with a bit with a different wording.

When the first submarines were built, they were very short ranged vessels, and were designed around their submerged operation. As such the very early subs, such as the first 'real' combat submarine, USS Holland of 1900, and it's immediate follow-ons, were actually more similar in shape to modern nuke boats than the wartime diesel boats of WWI and WWII.

These very early, tiny, coastal defense subs, from 1900 till just before WWI, had large, round, squat bodies, with very small conning towers. This design is best for underwater speed, and some of these early boats actually had faster underwater speeds than WWII subs!

But these early boats were meant only for local coastal defense - rapid dashes out to protect a harbor. No one cared for sea keeping qualities or surface handling.

And they were terrible on the surface. The round, squat shape that is ideal underwater is ill suited for surface operation. The drag was high. It would roll, a lot. It would pitch, and would be swamped by even small waves. The surface deck as slippery and treacherous. Venturing forth in any but the smoothest water was untenable.

That meant that these little harbor boats could not make long journeys over the open ocean - even for transport. Ocean patrolling was out of the question.

As subs developed further, several changes occurred. Diesels replaced gasoline engines, a much safer, less volatile fuel for confined spaces, and made carrying a large amount of fuel practical. The subs got larger, and soon became large enough for multi-day voyages.

Since a diesel sub needs to spend most of its time on the surface, it needs good surface keeping qualities to be able to venture out of a protected harbor into the open ocean.

Subs became longer and thinner in order to minimize surface wave drag and increase surface speed. The changed shape to a more 'ship like' cross section instead of the early sub's fat circle. The bow was raised up to help break through waves and keep from flooding the deck - and any open hatches. The deck became flat, with decking, to provide better footing on the open seas. The conning tower grew taller and larger to provide for a proper surface command and navigation center, with room for a bridge, AA guns, lookouts, periscope housings, radar antennas, etc. Deck guns sprouted to increase surface fighting power without using expensive and precious torpedoes. Antenna wires, handrails, periscope housings and other items began to clutter the deck.

By WWI subs had traded the early squat shape of their tiny progenitors for the needle-like shape that we are familiar with - a shape that did not basically change till the end of WWII. These needle-like boats were more high speed torpedo boats that could submerge in a pinch than true submarines. Their shape made them able to go on cross ocean voyages, and patrol the foulest weather seas, but subsurface performance was poor - low speed, lots of noise. A necessary compromise that, given the low power of the lead acid battery propulsion system they had to use underwater, was a wise choice.

Once subs returned to a totally underwater environment they reverted towards the squat, circular shape of the very early boats. At first the Germans, with their XXI, simply streamlined what started out as basically a typical surface U-boat design. But, as pointed out in other posts, when married with a powerful (ie: nuclear) underwater propulsion system, as in the USS Nautilus, the weakness of this halfway design was apparent, especially the instability at high speeds caused by the large flat deck.

The deck, a vital part of a old diesel boat that spent most of its time on the surface, actually helped the old diesel boats underwater - the large surface, with down angle on the boat, helped drive it deep in a crash dive. But at the high speeds of nuclear boats, a large flat deck was unstable and dangerous underwater.

The US then moved to the cylindrical shape in the diesel powered Albacore. Squat cylindrical bodies matched the pressure hull's shape, and were hydrodynamically efficient. The conning tower slimmed down to a mere sliver - for stability, and housing long periscopes, in US boats, and squat bumps on Soviet designs. Both were designed to minimize drag, and noise, in underwater operations. The deck, and other trappings of surface operations, disappeared.

The sub, finally married to the powerful underwater propulsion system it needed, returned to its roots as a vessel designed for underwater propulsion only.