C++ is often used for scientific programs. The popularity of C may be waning in that domain. Fortran remains popular as a “low-level” language.
In C++, “you only pay for what you use.” So there is nothing that would make it any slower than C. In particular for scientific programs, expression templates make it possible to perform some custom optimization using the template engine to process program semantics.
The reason C is preferred for projects such as Python is that it tends to be less confusing to read, so a large codebase will be more accessible to a larger pool of contributors.
SQLite has a requirement for small executable code size, where C does have a slight edge. Judicious use of C++ still allows use in embedded applications, but it is less popular due to fear that unwanted language features will creep in.