There is no relation between the sequence length and system performance. But when a short sequence is used, you see more fluctuations in the results as you repeat the simulation (for example if you use 100 bits and one bit is incorrectly received, you get BER=0.01, while one bit error for a seuqence of 10000 bits gives BER=0.0001). So it is as if the use of longer bit sequences improves the measurement accuracy somehow.