The problem is that in many cases you can't afford to sacrifice enough performance for it.
Also, malware and crypto doesn't "play in the same field". Malware is solved by secure programming, access controls and users that are educated to not fall for trojans.
Encryption handles communication and storage, and only to a small degree data processing.
On the other hand there are algorithms which are believed to be backdoored by the NSA (some elliptic curves). These algorithms can be avoided.
In the end, cascading encryption has very limited benefits because the weakest point of a security application is almost never the algorithm used.