Well, after many good answers explaining, while looking up the exact position of the virtual base class in memory incurs a performance penalty, there is a follow up question: "Can this penalty be reduced?" Fortunately, there is a partial solution in form of the (not yet mentioned) final keyword. In particular, calls from the class D of the original example to the innermost  base A can usually be (almost) penalty-free, but in the general case only, if you finalize D.
For why this is necessary, let's look at a multilevel class hierarchy:
class Base {};
class ExtA : public virtual Base {};
class ExtB : public virtual Base {};
class ExtC : public virtual Base {};
class App1 : public Base {};
class App2 : public ExtA {};
class App3 : public ExtB, public ExtC {};
class SuperApp : public App2, public App3 {};
Because our Application classes can use various of the Extension classes of our base class, none of those Extension classes can know at compile time, where the Base subobject will be located within the object, that they are called with. Rather, they have to consult the virtual table at runtime to find out. This is, because the various Ext and App classes can all be defined in different translation units.
But the same problem exists for the Application classes: Because App2 and App3 inherit a virtualized Base via the Extension class(es), they don't know at compile time, where that Base subobject is located within their own objects. So each method of App2 or App3 has to consult the virtual table to find the location of the Base subobject within their local objects. This is, because it is syntactically legal to later combine those App classes further, as illustrated with the SuperApp class in the above hierarchy.
Also note, that there is a further penalty, if the Base class calls any virtual methods defined on the Extension or Application level. That's because the virtual method will be called with this pointing to a Base object, but they have to adjust this to the beginning of their own object by again consulting the virtual table. If an Extension or Application layer (virtual or non-virtual) method calls a virtual method defined on the Base class, that penalty is incurred twice: First for finding the Base subobject and then again for finding the real object relative from the Base subobject.
However, if we know, that a SuperApp combining several Apps won't be created, we can improve things a lot by declaring the App classes final:
class App1 final : public Base {};
class App2 final : public ExtA {};
class App3 final : public ExtB, public ExtC {};
// class SuperApp : public App2, public App3 {};   // illegal now!
Because final makes the layout immutable, methods of the Application classes don't need to go through a virtual table to find the Base subobject anymore. They just add the known constant offet to the this pointer, when calling any Base method. And virtual callbacks at the Application layer can fixup the this pointer easily again by subtracting a constant known offset (or even not fix it up at all and reference the various fields from the middle of the object instead). Methods of the Base class also don't incur any penalty upon themselves, because inside that class, everything works normal. So in this three-level scenario with finalized classes on the outmost level, only the execution of methods on the Extensions level is slower, if they need to refer to fields or methods of the Base class, or if they are virtually called from the Base.
The backdraw of the final keyword is, that it disallows all extensions. You cannot derive an App2a from App2 anymore, even, if it doesn't require any of those Extensions. And declaring a non-final App2Base and then final App2a and App2b from it, would again incur penalties for all the methods in App2Base, that refer to the original Base. Unfortunately, the C++ Gods didn't give us a way to just unvirtualize a base class, but leave non-virtual extensions possible. They also didn't give us a way to declare a "master" Extension class, whose layout stays fixed, even if other Extensions with the same virtual Base class are also added (in this case, all the non-master Extensions would refer to the Base subobject within the master Extension).
The alternative to virtual inheritance like this is usually to add all the extension stuff to the Base class. Depending on the application, that might require a lot of extra and often unused fields and/or a lot of extra virtual method calls and/or a lot of dynamic_casts, which all come with a performance penalty, too.
Also note, that in modern CPUs, the penalty after a mispredicted virtual function call is much higher than the penalty after a mispredicted this pointer fixup. The first needs to throw away all results obtained on the wrong execution path and restart afresh on the right path. The later still needs to repeat all opcodes depending directly or indirectly on this, but doesn't need to load and decode instructions again. BTW: The speculative execution with unknown pointer fixups is one of the reasons, why CPUs are vulnerable to Spectre/Meltdown type data leaks.