How many sequences can HOMER handle?
In theory, a lot (i.e. millions). It has been designed to work well with ~10k target sequences and 50k background sequences. If you are using a large number of sequences with findMotifs.pl, you many want to use the "-b" option, which switches to the cumulative binomial distribution for motif scoring, which is faster to calculate and gives essentially the same results when using large numbers of sequences. The binomial is used by default in findMotifsGenome.pl. (I guess it should be called BOMER !?).
