Comment 3 for bug 1210280

This appears to be a setting in glibtop/cpu.h:

https://developer.gnome.org/libgtop/stable/libgtop-cpu.html#GLIBTOP-NCPU:CAPS which becomes an array size and only GLIBTOP_NCPU are gathered.

From the source package: libgtop2:

cat -n
 ...
    53 /* Nobody should really be using more than 4 processors.
    54 Yes we are :)
    55 Nobody should really be using more than 32 processors.
    56 */
    57 #define GLIBTOP_NCPU 32
    58
    59 typedef struct _glibtop_cpu glibtop_cpu;
    60
    61 struct _glibtop_cpu
    62 {
    63 guint64 flags;
    64 guint64 total; /* GLIBTOP_CPU_TOTAL */
    65 guint64 user; /* GLIBTOP_CPU_USER */
    66 guint64 nice; /* GLIBTOP_CPU_NICE */
    67 guint64 sys; /* GLIBTOP_CPU_SYS */
    68 guint64 idle; /* GLIBTOP_CPU_IDLE */
    69 guint64 iowait; /* GLIBTOP_CPU_IOWAIT */
    70 guint64 irq; /* GLIBTOP_CPU_IRQ */
    71 guint64 softirq; /* GLIBTOP_CPU_SOFTIRQ */
    72 guint64 frequency; /* GLIBTOP_CPU_FREQUENCY */
    73 guint64 xcpu_total [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_TOTAL */
    74 guint64 xcpu_user [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_USER */
    75 guint64 xcpu_nice [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_NICE */
    76 guint64 xcpu_sys [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_SYS */
    77 guint64 xcpu_idle [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_IDLE */
    78 guint64 xcpu_iowait [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_IOWAIT */
    79 guint64 xcpu_irq [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_IRQ */
    80 guint64 xcpu_softirq [GLIBTOP_NCPU]; /* GLIBTOP_XCPU_SOFTIRQ */
    81 guint64 xcpu_flags; /* GLIBTOP_XCPU_IDLE */
    82 };
    83
...

So, in short, System Monitor is not designed to be the official reference for CPU counts.
I've filed a bug against the Ubuntu/Debian package.
Running gnome on a 64 core machine is a bit odd--they are typically used as headless servers.