With a permanent cloud cover, you'd have no astronomy and much of the impetus that it gave general science during the ages. As for flying above the clouds, there is no guarantee that aircraft would ever be developed that could do that (depending on the ceiling and depth of cloud cover.

With a solid, deep cloud cover, I can easily see a world in which the sciences never develop past the bronze age or so. The astronomical calendars for determining the Solstices and equinoxes, the ability to navigate at sea (and the consequent exploration and development THAT brings), and a host of other crucial technology drivers along the development of a technological civilization simply would never have existed. From a more "fuzzy" point of view, the Sun and the Moon and the stars have driven human development. Knowing the Sun moved in its path through the sky in a pattern which was predictable and linked to the seasons led to methods to track and predict that movement. The Moon and the stars were sources of wonder, leading to development of devices to view and monitor them. Astronomy was a driver in the development of mathematics, as astronomers (many of them mathematicians) sought to describe mathematically what they saw, particularly the movements of the planets.

Back to the aircraft. Presuming that you got as far as developing some type of flying machine (itself not a given, but if you did get that far, lets start with a balloon), you have to have someone who 1) believes that there MIGHT be something up there to see, and 2) who manages to build a balloon large enough and with enough lifting ability to get above the cloud deck. Getting a balloon up through a thick cloud layer, particularly if there are convective clouds around, becomes a dangerous way of exploring the heights.

A heavier than air craft is an extremely unlikely candidate for the first penetration of clouds in this case, for a few reasons. First, unless the clouds are rather high, you aren't going to develop large aircraft capable of getting very high in the first place. Secondly, until you do that, and develop the instrumentation necessary to safely fly under such conditions, you aren't going to be able to safely fly into the clouds to get above them. Early aircraft were developed and flown in clear weather, and only then did instruments, etc., get developed to fly (and navigate) them in poor visibility (to include night flying to some extent). Aircraft had to be developed with the performance (range and time aloft primarily) to make this a factor before any solution was developed.

Mike