Q. In some shuls it is customary that the rabbi or the gabbai, at the end of shacharis recite without a bracha the sefira of that day. Is this not a case of b'al tosif or prohibited adding to a mitzva, according to those that maintain the mitzva is complied only at night, and thus should be avoided?
A. Kaf Hachaim (489: 80) writes that it is a proper tradition, that every morning before or after shacharis, the shaliach tzibur should mention the count of the omer; in case someone forgot to count on the prior night.
Minchas Yitzchok (6: 45) quoting several great Chassidic authorities, relates that these Tzadikim would mention many times every day, the omer number of that day. Thus giving a different perspective to the meaning of "Temimos" or complete days. Moadim Uzemanim (7: 230) debates whether Hagr'a would maintain that you comply with the mitzva every time the count is repeated, as he maintains on eating repetitive kezais of matza during the days of Pesach.
Poskim maintain that there's usually no prohibition of b'al tosif when repeating a mitzva several times. Tosafos Rosh Hashana 16b in reference to blowing additional times the shofar on Rosh Hashana or holding the lulav several times a day in Sukos. Turei Even disagrees (ibid.)
Igrois Moshe (O.H. 2: 60) debates if there is a prohibition of b'al tosif when davening maariv before the z'man, if one recites the shema too early with the intent to fulfill the mitzva. He therefore stresses one should have intent not to fulfill the mitzva at that time. He also argues that Shema is essentially a part of Torah learning and there's no prohibition to learn Torah multiple times.
(See Chavos Daas - Beis Hasofek, Safek Safeka: 20, opines, that repeating Shema twice, even within the obligated time is prohibited).
The Sephardic minhag to repeat sefiras haomer in the mornings (Yalkut Yosef 489: 25).
However, Teshuvos Vehanhagos (O.H. 1: 312, 2: 247) indeed writes that the reason (Ashkenazim) do not usually repeat the sefira in the mornings is because, as some Poskim maintain, there may not be a mitzva complied with during the day. Therefore, if one does not have in mind that his counting is conditional to there being a mitzva involved, he would transgress in the prohibition of b'al tosif. He adds that not all people are mindful of having in mind this condition.
Horav Shlomo Miller's Shlit'a opinion is similar and if one has the tradition to repeat, he should have in mind that condition.
Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit'a