the typical rule is that you'll need to "activate" the 3in1 somehow before the DS recognizes it. Give it a test and see if you can load something like a legitimate metroid pinball DS cart without patching and see if rumble works with 3in1. Most likely not.
The code provided by EZ team to allowed third-parties to do so. CycloDS has integrated the code into their firmware, R4 hasn't so far... so you need to load rudolph's tool to activate (when you do, it'll soft reset back to your games list in the R4). Of course, this does not mean that you're patching the nds files themselves. You have to read the EZ forums to see what's happening under the hood. I'm no expert
edit: I also forgot that there IS a patching tool that can detect the 3 in 1 rumble without using Rudolph's tool. That's another option. There's a link in the wiki. Open source is awesome!
I think I accidentally removed chuckstudio's tool from the wiki, but it's back up in the third-party software section.