Learn Turkish: Uygulamaları güncellemenin zahmetli bir süreç olduğunu sanıyorlar. - They think that updating the applications is a laborious process.

This is part of the embedded noun clause. In the English phrase 'that updating is a process', 'updating' is the subject of that sub-clause. In Turkish, the subject of a -dIk clause takes the genitive case, linking it to the possessed verb olduğu. Literally, it forms a structure like 'updating's being a process'.

Why is the accusative suffix used twice here, in uygulamaları and olduğunu?

Each accusative suffix connects to a different verb. Uygulamaları (the applications) is the specific direct object of the verbal noun güncelleme (updating). Meanwhile, the entire phrase becomes the direct object of the main verb sanıyorlar (they assume), which requires the accusative case on olduğunu (that it is).

Why use sanıyorlar here instead of düşünüyorlar?

While both can translate to 'they think', sanmak implies an assumption, a guess, or a belief that is often incorrect. By using sanıyorlar, the speaker strongly hints that updating the apps is not actually that laborious. Düşünüyorlar would just state their opinion neutrally.

Could I form this sentence using ki instead?