If you use ByteBuffer, then yes, the application may suffer from unnecessary checks. However the performance of ByteBuffer is not usually good enough anyway, that's why people use off-heap buffers (sun.misc.Unsafe) which is a native call that allocates memory in off-heap.

Also bytecode has instruction sets for all primitive types, otherwise there wouldn't be any point to have these primitive types in Java language since it will also be converted to bytecode instructions.

There are solutions for all the addressed issues but they need to much work to implement in Java compared to C++. However, once you solve this specific problem (I admit that it's not a small one), there are lots of benefits of using Java compared to C++.