It's not a foolish question , Keva - just a misleading video.
1. There are many different accents within the British Isles, and it is most definitely UNTRUE to say that British people 'always' pronounce 'water' with a glottal stop. While the typical working class London accent, for example, does have this feature, it is by no means universal. Only a tiny proportion of the population would pronounce 'water' as /wɔː ə/. The majority of British people, whatever their accent, would pronounce this word exactly as the dictionary shows, with a clear 't' : /wɔːtə/.
2. If by glottal stop, they mean that the 't' is not fully pronounced, then yes, this is normal. If you hear someone say 'I can't go', then the 't' sound is barely audible. But this has nothing to do with British accents - it is a feature of speech that applies to all English speakers.
As for whether this causes confusion with 'can', then no, not at all. If you check in your dictionary for the standard British pronunciations of 'can' and 'can't', you will see that these words are very different indeed. 'Can' is pronounced /kæn/, while 'can't' is pronounced /ka:nt/ with a long 'a'. This long /a:/ in 'can't' is a particularly noticeable feature of standard British English, and there is never any confusion between the two words.
In fact, foreign learners are far more likely to confuse 'can' and 'can't' in American English, where the two words do have the same vowel sound. Native speakers, needless to say, don't get confused, because the native speaker ear will pick up clues from the context, stress and intonation of the sentence to know whether it is positive or negative.
By the way, can you send us a link to this video? I'd like to know what other misleading things it's telling people.