i get this problem too,messages from my contacts don't always show up on every device yet these are established contacts that i have been messaging for some time,i put it down to iMessage still being in beta and prone to problems.Sometimes iMessages come through on both iPad & iPhone but other times only on one of them. Why?
everyone i iMessage use my email but even then there are times when they don't appear on my 4s,as i say i put this down to beta as its intermittent.It's not about your contacts on your device but what the people messaging you are using. If they use your telephone number then the iPad won't get it.