Thanks for the reports! 
In reference to:
"-I've found that the Missionary Center benevolence improvement does not actually seem to provide the promised ideology points. I've constructed one on most of my worlds and my ideology meter hasn't moved an inch. A source of a great deal of frustration since I was counting on those to provide additional ideology points since I'm running out of planets in my current game..."
"-Lag spike when revealing new planets on the galactic map."
"-On occasion, when I do things in the ship yard, the queue doesn't seem to update until I close and reopen that shipyard screen."
Would you kindly, submit a ticket via our support system so that I can better assist you with your issues. After following the link, run the support tool, include your steam name, save files before the issues happening(if possible), describe the issue you are having and then send us the zip file to greatly speed up the process!
Link to forums for explanation:
https://forums.galciv3.com/452855/page/1/
Link to support tool:
http://sd.stardock.com/Support/supportToolTest/SDSupportTool.exe