As far as I know mitzvot such as eating marror or saying hallel at the Pesach seder are only rabbinic (the marror was biblical previously but I am told that is no longer so). If this is the case and if it is the case that the second day of Pesach is treated as a yom tov (in the diaspora) because of a safek (doubt) and furthermore if we apply the principle of 'safek d'rabbanan l'kulah' - why then do we make blessings on the mitzvot at the seder which are rabbinic?
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If Yom Tov sheni was dealt with differently, in ways that treat it on a lower level due to it's being a safek, people would not respect it as much. Therefore, Chazal instituted all the same observances in order to give it the prestige of a normal Yom Tov. Not making the blessings would degrade the status of the day.
The main reason given for saying a bracha on a derabbonon is that you are mekayem the mitzvah of 'Lo Tasur' (you shall not deviate from what they command you). We have this now in the daf yomi, Sukkah 46a, as a result we still make a bracha on lulav, matza, megilla and others. Note that in the discussion on the daf, we do not bring up the question of saying the bracha because of 'safek derabbanan' in any way. This can be found in many discussions of the halachos of these mitzvos.
The safek is not a matter of 'safek bracha', that is, we are not in doubt whether or not the bracha should or should not be made. This is a situation of 'safek yom' which we see from the discussion in the gemoro is to be treated as yom tov. That is why we daven the yom tov prayers, have the seder, etc. Once we do that, then we consider the brochos as not a safek.