The plural of the noun hypothesis should always be hypotheses. This is not just because it is hard for a native English-speaker to say 'hypothesises': it is because 'hypothesis' was originally a Greek word, and academics should respect the traditional forms. In Latin, through which English took the Greek, the regular plural of nouns ending in 'is' was the ending 'es'.
To make it clear when you are using a plural and when you are using a singular, pronounce the plural with a long '-ee-' vowel. This attracts rather more stress in the pronunciation than the final vowel in the singular.
The word 'hypothesises' does exist: it is the third person singular of the verb 'to hypothesise'. It may help to distinguish between the noun and the verb by spelling the verb as hypothesizes and the noun, with its different pronunciation, as hypotheses (You may also want to see hypothesises (pronunciation).)
- Hypothesis is one of the 117 mis-spellings listed as 'Common difficulties' in the section on 'Spelling' within 'Writing' in UEfAP.
See also hypothesis - pronunciation