Just checked mega 3.0 on builds 26587 and 28072 for the e3000.
There is no jffs2 on the web gui Administration page. _________________ Asus ac87u - DD-WRT v3.0-r28139 std (11/13/15)
Asus ac68r - DD-WRT v3.0-r28139 std (11/13/15)
Asus ac66u - DD-WRT v3.0-r28139 (11/13/15) giga
Linksys e4200 v1 - DD-WRT v3.0-r28139 (11/13/15) mega
in previous dd-wrt i just enabled JFFS2, selected "clean", restarted the box and I had a write-able jffs folder on the router to use for small scripts. But now that option has vanished, and I think by mistake.
I cannot find any writeable folder now on the router to put my own scripts into (like a script for IPV6 6rd)
I have used dd-wrt on Asus RT-N12D1, Belkin F5D8235-4 v2 and both of them don't have jffs2. I also used dd-wrt on EA6500 v1 but I am not sure if jffs2 is supported since I only used dd-wrt on it for a few weeks last year and since then reverted back to stock and I can't recall if jffs2 is available. Hence, I think missing jffs2 is not an uncommon thing for dd-wrt. I have a WNR3500L v2 which is using Tomato Shibby and it has jffs2. Hence Tomato Shibby may be another option for your E3000. However, I believe jffs2 may still be available for dd-wrt on other routers but I don't know which routers still have it.
If you still like your E3000 and dd-wrt since you have more experience on it, I think using a small USB thumb drive may be the most viable solution for you at present.
If I am not wrong, I think v3 with Kernel 3+ support max disk size of 4TB. However, Samba on dd-wrt is not very good and you probably won't get a decent NAS speed due to limited RAM & CPU power of E3000. Hence, I suggest you give it a try first before investing on a large USB drive. As for NTFS support, you better check it as well. It may support NTFS since E3000 has 8M of Flash.