The reason boils down to English stress patterns.
Science is stressed on its first syllable and the vowel/diphthong in stressed syllable is strong so it's pronounced /ˈsaɪ.əns/.
Another example is scintillating which is stressed on the first syllable so it's pronounced /ˈsɪntɪleɪtɪŋ/.
On the other hand, the monosyllabic prefix con- bears the primary word stress so when it's added to the word science, the primary stress from the word science moves to the prefix con- therefore conscience is stressed on the first syllable and is pronounced /ˈkɒnʃ(ə)ns/ not /ˈkɒn.saɪ.əns/ (the vowel in unstressed syllable often reduces).
The /ʃ/ sound is due to Yod-coalescence.
Other examples are:
- Extension -> /ɛkˈstɛnʃ(ə)n/.
- Social -> /ˈsəʊʃ(ə)l/.