yeah, i'm having the same problem. in pre-ICS versions of android, you could click "Yes" in the email and it would add the event to your calendar. First, make sure you have your calendar notifications set up correctly -- go to your google calendar from your computer, go to calendar settings, click the Calendars tab, and click the notifications link next to your main calendar. Make sure you have it set to send you an email for all the events (except daily agenda, optional). Actually, as I was typing this, I did some experimenting and figured some stuff out:
If the meeting organizer has shared their calendar with you, AND you have a check next to their calendar in your phone's calendars to sync, then clicking "Yes" in the invitation email will open *their* version of the event in Calendar, and you don't have the options to accept the meeting and add it to your calendar. I guess google figured that if you're syncing their calendar, you don't need to duplicate it in your own calendar. You do still have the option here to add a reminder so you will be notified when their event takes place. But that still doesn't let them know whether you accepted or not.
I found a workaround for this problem. Go back into your Calendar Settings on the web site from your computer. On the general tab, scroll down and look for "Automatically add invitations to my calendar:". Select either of the "yes" options. I selected "Yes, but don't send event reminders unless I have responded "Yes" or "Maybe"". Save your settings and then refresh your calendar on your phone. Now, when you get invited to a meeting/event, open your Calendar on your phone and navigate to the event date. You should see an empty box with just an outline (instead of the regular color-filled box). This is an unaccepted event. If you click on this event, you should have the options to set your attendance status.
The other "solution" is to uncheck that person's calendar in your phone's calendars to sync. If you do that, you will be able to click "Yes" from the invite email like normal.
I'm gonna look around to see if anyone has reported this issue to google. I definitely think you should be able to easily accept an invitation from someone that you also sync calendars with. Definitely seems like an oversight. Hope this helps.