Upgrading on a MATX board tends to be a case of replacing rather than adding on, because the size limitation usually means fewer available PCI and RAM slots. What you need to add on will also be defined by the board, many come with integral LAN & USB sockets and onboard sound and graphics leaving more choice as to what to fit in the available slots.
The ability to upgrade your processor is not affected by the physical size of the mother board, the boards develop in tandem with the chips and a new small mobo will take a faster processor than an old large one. If you look at the MOBO manufacturers website you should be able to find out what range of chips will fit the board.
As to MATX cases, some are smaller than others being limited to 1 or 2 5.25" bays and a 3.5". Others are more generous. It's down to personal choice, how many drive bays do you think you'll need ? Some people find a 3.5 floppy and a combi drive sufficient. Others want tape drives and integral card readers. Only you will know if the case is big enough.
Post details of what you're looking at maybe somebody here already has one and can give their views on it.