Hellas,
did you check that those connections really are from/to amule? On my box, I currently have 396 lines in conntrack, but not all of them are amule-related.
A rough estimate can be calculated as follows (assuming 4662 is your amule tcp port number):
cat /proc/net/ip_conntrack | grep "sport=4662" | wc -l
# Connections from amule port, here: 141
cat /proc/net/ip_conntrack | grep "dport=4662" | wc -l
# Connections to amule port, here: 139
cat /proc/net/ip_conntrack | grep "dport=4662" | grep "sport=4662" | wc -l
# Connections with both ports set to 4662, here: 140
Now add the first two numbers, and substract the third - 140 Connections.
You could also try netstat -anp | grep amule | grep tcp | wc -l , which gives here a count of 56 . The remaining 84 seem to be in state "TIME_WAIT", which means that they are half-closed. The kernel needs to track them until they cleanly shut down (or expire), but apparently amule does not count them as active connections, since they are already closing.
Best regards,
-hannes
[edit: moved comments on separate lines]