Converted carriers were relatively common in the early period of carrier development. It was a lot cheaper and quicker to take a hull that was already existing, and build a flight deck on top of it, than it was to build one from scratch. The British carriers Argus, Eagle, Furious, Courageous and Glorious were all conversions, similar to Akagi and Kaga (though Argus began her life as a liner rather than a battleship). The Americans did the same with the Lexington class. Similarly, the Italians began, though never completed, the conversions of two liners to carriers, while the IJN did complete two such conversions as the Hiyo-class. With Akagi and Kaga, the two hulls began construction in 1920. By 1922, when the Washington Treaty was signed, the hulls were essentially complete, and work was beginning on fitting them out. The WNT stated that the IJN could convert two ships, from either their new construction or existing ships, to carriers - and it made most sense for them to convert new builds, as that wouldn't reduce their battleship strength. Originally, Akagi and her sister Amagi were to be converted, maintaining commonality between the classes. However, the Great Kanto Earthquake of 1923 irreparably damaged Amagi's hull, meaning that Kaga had to be substituted. Kaga's sister ship, Tosa, was more complete, meaning that conversion to a carrier would have cost far more, as it would require removal of the turret barbettes and similar fittings.

Unlike Akagi and Kaga, Hiryu and Soryu were purpose-built as carriers. They were originally intended to be sister ships, and were ordered as such under the 1931-2 Naval Armaments Supplementary Program. While they were under construction, several events revealed weaknesses in Japanese naval design. In 1934, the torpedo boat (small destroyer) Tomozuru was capsized in a storm, thanks to high topweight. In 1935, the Fourth Fleet sailed into a typhoon, in what would become known as 'The Fourth Fleet Incident'. The fleet took heavy damage - two destroyers lost their bows, a third nearly lost her stern, two cruisers and a minelayer suffered severe hull distortions, and the light carriers Hosho and Ryujo took damage to their bridges and flight decks. The lessons learned from these incidents were digested, and applied to the carriers under construction. However, Soryu was considerably more advanced than her sister, meaning that opportunities to modify her design were limited. To solve the problems that the Fourth Fleet Incident made clear, Hiryu had her beam increased, her armour increased, her hull strengthened and her bow redesigned. These changes made her different enough to Soryu that she can be considered as a separate class, despite the clear lineage.

As to whether this made the ships harder to supply and maintain, that's not really the case. In the 1940s, ships commonly had different hull structures and designs, even within a single class. Hull plates and fittings were typically produced on a bespoke basis, as and when they were needed. The main determinant of logistical burden were the engines and armament. Hiryu and Soryu had the same powerplant and armament, and shared features of both with Akagi and Kaga. All four ships used similar boilers, and were armed with identical 25mm light AA guns (though the 127mm AA guns on the later ships were incompatible with those from the earlier ships). This meant that IJN logistics weren't significantly impacted by having to support a plethora of classes.

To add a little bit to /u/thefourthmaninaboat here:

Carrier conversions typically result in design compromises that are usually not present in purpose-built carriers like Soryu. In the case of Akagi and Kaga, these ships' performances suffered somewhat as a result of these compromises. Of the two ships, Akagi's was the more successful conversion. Kaga's battleship hull form and machinery meant that she suffered from a top-limit on her speed, which was problematic for carriers as they need high speed to facilitate air operations. Her 1935 modernization lengthened her hull and improved Kaga's machinery, but she was the slowest of the IJN's fleet carriers at the start of the war with a homely 28 knots as her approximate top speed. By way of comparison, Soryu could make that speed at 40% of her machinery's power. Akagi fared better, since her battlecruiser hull was designed for high-speeds, but she too had compromises. Like Kaga, Akagi's machinery was inefficient for the results achieved and both ships used more fuel than their purpose-built stablemates.

BB/BC conversions also suffered in the legacies of their surface ship origins. In common with other navies, both carriers initially had a strong anti-ship armament to protect against cruisers and destroyers. In practice, all three carrier -heavy navies (IJN, RN, USN) found that large gun armament was near useless on a carrier and began the process of deleting them in various reconstructions. Both Akagi and Kaga though had vestigial remains of these experiments in the form of casemated 8-in guns near the waterline. This was dead weight and functionally useless. Had both carriers survived Midway, it was likely that their refits would have removed these guns. Another problem conversions had was exhaust. The layout of the machinery imposed certain limits on where and how to place the exhaust machinery. On BBs and BCs, this was a simple matter of a vertical smokestack, but it was not practical to have one in middle of the flight deck. Akagi and Kaga pioneered the initial IJN approach of having hull-side exhaust ducting, but this produced problems. Hot exhaust gases made operations adjacent to them unbearable and Japanese naval constructors recognized this. One of Kaga's proposed reconstructions after the Fourth-Fleet incident included an upturned exhaust. But such reconstruction was difficult and the hulls had very little flexibility to adapt to these changes. Later IJN carriers solved this problem through either staging the exhaust through several side-funnels or having a vertical smokestack incorporated into the island.

But these compromises did not fundamentally impact the overall success of these two conversions. The learning curve for the first generation of aircraft carrier design was fairly steep and the IJN avoided some of the problems that bedeviled the British carrier program. RN conversions were often on smaller-hulled warships like the Courageous-class light battlecruisers which in turn placed a limit on how small an airgroup they could field. Akagi and Kaga were large hulls that could incorporate the changes needed to meet the demands ever more sophisticated carrier aircraft, albeit at times inefficiently.