I looked at one trace and the blocking leads to the libmysqlclient:

#0  0x00007fa250dd3730 in futex_wait (private=<optimized out>, expected=0, futex_word=0x7fa2523a2d1c) at ../sysdeps/unix/sysv/linux/futex-internal.h:61
        __ret = -512
        err = <optimized out>
#1  futex_wait_simple (private=<optimized out>, expected=0, futex_word=0x7fa2523a2d1c) at ../sysdeps/nptl/futex-internal.h:135
No locals.
#2  __pthread_rwlock_wrlock_slow (rwlock=0x7fa2523a2d10) at pthread_rwlock_wrlock.c:67
        waitval = 0
        result = 0
#3  0x00007fa251b11d30 in ?? () from /usr/lib/x86_64-linux-gnu/libmysqlclient.so.20
No symbol table info available.
#4  0x00007fa2510468e7 in CRYPTO_add_lock () from /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
No symbol table info available.
#5  0x00007fa251466cfc in SSL_CTX_free () from /lib/x86_64-linux-gnu/libssl.so.1.0.0
No symbol table info available.
#6  0x00007fa251468ff0 in SSL_free () from /lib/x86_64-linux-gnu/libssl.so.1.0.0
No symbol table info available.
#7  0x00007fa24ef6a38a in tls_h_tcpconn_clean (c=0x7fa2535b8998) at tls_server.c:655
        extra = 0x7fa2535ca9c8
        __func__ = "tls_h_tcpconn_clean"
#8  0x00000000004ed791 in _tcpconn_free (c=0x7fa2535b8998) at core/tcp_main.c:1352
        __func__ = "_tcpconn_free"
#9  0x00000000004ff708 in tcpconn_put_destroy (tcpconn=0x7fa2535b8998) at core/tcp_main.c:3030
        __func__ = "tcpconn_put_destroy"

Can you get the output for:

ldd /usr/lib/x86_64-linux-gnu/libmysqlclient.so.20

There were couple of similar reports for ubuntu 16.04 with security updates, having issues when connecting to mysql server via IP sockets. You can check the latest commits to db_mysql module done in master branch (backported to 5.3, iirc), among them leading to addition of opt_ssl_mode parameter. You can try to connect to mysql via unix socket file, if you have the mysql server on the same system as kamailio (use localhost instead of 127.0.0.1 in db url). I spent quite some time analyzing such a similar issue on ubuntu 16.04 with security updates, trying to track changes in libssl/libcrypto and libmysqlclient, but at the end the solution was to upgrade ubuntu not to have a mixture of libraries built with libssl1.0 and couple of them with 1.1.

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