to install an old orthography Malayalam Unicode font which is required to read the posts below]
ZWJ & ZWNJ are supposed to be font directives, directing a font to select from two or more sematically same renderings. In case of Malayalam, this is no longer true. ZWJ becomes an alien language construct introduced to Malayalam language by Unicode to produce ചില്ലക്ഷരങ്ങള്. Thus, it is possible to produce 2 semantically different words which differ only by ZWJ in its Unicode representation. Eg: അവന് & അവന്.
When a word is searched in Unicode text, the search algorithm should ignore ZWJ & ZWNJ for it shall not care about the rendering of the word. From the above reasoning, that does not hold good for Malayalam. But, if does not ignore ZWJ & ZWNJ, then it surely is going to missout on some words which are sematically same but rendered differently by using/omitting ZWJ/ZWNJ.
Because of this ZWJ & ZWNJ 'ad hoc fix' for Malayalam, a minor issue also pops up: an encoding can not give the font the freedom to choose between conjunct form or virama seperated form - as in other Indian languages. Example: no way to allow font to choose between ന്മ ന്മ. For Malayalam only, ന + virama + മ should always prefer ന്മ conjunct because ന + virama + ZWJ forms ന്.