Amilcar Cabral was the leader of the political group PAIGC (African Party for the Independence of Guinea and Cape Verde). So, his role was as independence leader for both Guinea and Cape Verde, and in fact PAIGC cadres were more active and more successful at creating "free zones" in Portuguese Guinea before independence in 1975.

I am not particularly informed about Czech intelligence services, so I will need to do some more research on the specifics of that organization before I can comment specifically.

However, generally, the orientation of Czech and other Eastern Bloc countries followed the Soviet line in terms of of foreign affairs with African countries. Elizabeth Schmidt notes in her book Foreign Intervention in Africa from the Cold War to the War on Terror that Czechoslovakia sometimes served (with Soviet blessing/encouragement) as an arms seller to friendly third-world regimes like to Nasser's Egypt in 1955. She calls Czechoslovakia "the Soviets' primary weapons conduit".

Was the Czechoslovak foreign service uniquely internationalist, or did other Eastern European socialist countries play an active role in liberationary movements like Cape Verdean independence?

Did the Czech Republic have any specific motives for supporting the independence of Cape Verde, out of all the colonized countries in Africa?

In general, socialist/marxist aligned governments of the Soviet Union, the Eastern Bloc, Yugoslavia, China, and Cuba all spoke a great deal about the Anti-colonial or anti-Imperial struggle going on in Africa. Again, Eastern Bloc governments tended to follow the Soviet line in terms of providing military training or material support to anti-colonial movements, while China, Yugoslavia and Cuba all tended to enjoy greater freedom to take their own line. In fact, throughout the 1950s, 1960s and 1970s, the Chinese often acted almost as rivals to the Soviets, by supporting different political parties and armed groups than Soviet-sponsored groups.

In the specific case of PAIGC, Schmidt says (page 90) that Cabral made a tour of socialist countries in 1960s and was able to secure military training and weaponry from Czechoslovakia, Cuba, and China, as well as OAU members Algeria, Morocco, Ghana and Guinea(Conakry) which supported PAIGC as part of the Organization of African Unity's commitment to the independence of all European colonies in Africa.

So, as early as 1960 you see both the Chinese camp and the Soviet camp (in Czechoslovakia and Cuba) supporting Cabral's movement.

It's also worthwhile to remember that by 1962 or 1963, nearly all of the French and British colonies in Africa had gained independence. What was left were Guinea and Cape Verde, Angola and Mozambique as the colonies of the Portuguese colonial empire, as well as the white minority-rule states of Rhodesia and South Africa. In that context, Czech interest in Guinea and Cape Verdean independence loom larger as ways to forge ties with Cabral's presumed post-independence government, but also to demonstrate Eastern Bloc fraternal solidarity in the anti-colonial struggle (for the broader African audience).

So, why was Czechoslovakia involved with Cabral but not the Soviet Union directly? Again, I expect to research a bit more, so I might change my answer, but I feel somewhat comfortable speculating that the Soviets felt that they had not-unlimited military/economic/diplomatic resources to devote to third-world liberation. So, the Soviets probably decided to focus their efforts on building relations with the MPLA, since Angola was/is a larger, more populous, economically more important colony/country than Guinea or Cape Verde. (so, independence of Guinea and Cape Verde was important symbolically in the anti-colonial struggle, but not so important as Angola or Mozambique)

We can see this sort of decision making later, in remarks made by Fidel Castro to Ernest Hoenniker in 1977:

There were several requests for military aid from various sides: [Libyan Leader Moammar] Qadaffi, Mengistu, and the Congolese leaders. During our stay in Africa we sent [Cuban Vice President] Carlos Rafael Rodriguez to Moscow to confer with our Soviet comrades and to Havana for consultations with our leadership. In order to find the best solution we must think through this question calmly and thoroughly and consider it in terms of the overall situation of the socialist camp.

I am assuming (I think reasonably) that Soviet and Eastern Bloc governments would have faced the same dilemma of multiple requests for support in the 1960s and early 1970s, and so Cabral may have been put into the Czech intelligence service's "portfolio", to free up the Soviets for larger/more strategic initiatives.

I'll try and hunt down a better answer for you.