Most EZFlash saves should be raw saves. The main ones that won't be are some (third party but never the less popular, the names escape me right now though) managers for the 3 in 1 (originally an expansion pack for DS carts but was made open source and got quite popular) added either a header or a footer to them. Simple detection there being not a normal power of 2 size. There are a few threads and tools around here to fix that and detail things (some combo of ezflash header footer save should bring them up).
Any issues normally being picky emulators, tricky names (all official EZFlash stuff went for the file name rather than header/serial based stuff of some emulators and flash carts), size trickiness (see old VBA and Flash sizes vs homebrew vs pokemon), user error (wrong region), corruption (batteries, kernel issues, ROM issues and turning off too soon) or going to other custom formats that did use headers/footers (said headers/footers usually being at best a file name and at worst for the average user and potentially your save conversion efforts some serial and header values*). As far as VBA is concerned then file - import - battery save or whatever it was tending to do me just fine.
*serials are not always unique so sometimes regions, revision number and more come into play.
Some DS stuff was potentially tricky with earlier EZ5 kernels -- they had a save list where everybody else/the R4 that everybody copied defaulted to just assuming 512 kilobytes (while we still were dealing with 2 gig max SD at this point it was considered an acceptable loss for the drag and drop but update every other day vs 2 clicks in a menu and continued supporting games for years afterwards with no update strictly necessary crowd). To that end the saves of earlier EZ5 stuff might well have been the actual size of the game's save rather than padded out. Think some of the EZ4 DS mode saves defaulted to 256 KB rather than 512 or some variation on that theme -- other than Daigasso Band Brothers, Art Academy, Jam with the Band, Warioware and I think there was another most things topped out at 2Mbit but things measured in kbits stuck around until the end). You can poke around
http://www.advanscene.com/ or some ROM list if you want, such things might even give you a header value and size list if you wanted.
I am not aware of any save compression being employed for anything. Mostly no$gba and possibly the DSx going in for that.
GB and GBC stuff might get fun depending upon what goes. Their only GB/GBC effort is the comparatively recent EZFlash Jr. Everything before then (including the Omega line) will be a wrapper for the goomba emulator at some level which means you are better served playing with that instead. It should be open source so easy enough to sort there (don't think they will be simple concatenation but also don't know the format).
After that it is pretty much going to be savestates or save editing for early EZ4 stuff (they dumped a version of their own firmware rather than the user's for DS mode and hence names/favourite colours/birthdays/... might not have been respected for those DS games that cared).
I can scare some up later if you really want though.